PDB Short entry for 5MCW HEADER TRANSCRIPTION 10-NOV-16 5MCW TITLE NEW INSIGHTS INTO THE ROLE OF DNA SHAPE ON ITS RECOGNITION BY P53 TITLE 2 PROTEINS (COMPLEX P53DBD-LWC2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: P53 DNA BINDING DOMAIN; COMPND 5 SYNONYM: ANTIGEN NY-CO-13,PHOSPHOPROTEIN P53,TUMOR SUPPRESSOR P53; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: DNA; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TP53, P53; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET27-B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 OTHER_DETAILS: SYNTHESISED BY IDT KEYWDS TRANSCRIPTION, P53, TRANSCRIPTION FACTOR, DNA BINDING, DNA KEYWDS 2 RECOGNITION, WATSON-CRICK BASE-PAIRING, INOSINE, 5-METHYLCYTOSINE, KEYWDS 3 TRANSCRIPTION REGULATION, APOPTOSIS, BIOLOGICAL RHYTHMS, CELL CYCLE, KEYWDS 4 NUCLEUS, TUMOR SUPPRESSOR, ANTIGEN NY-CO-13, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.GOLOVENKO,H.ROZENBERG,Z.SHAKKED REVDAT 4 17-JAN-24 5MCW 1 REMARK REVDAT 3 02-JAN-19 5MCW 1 TITLE JRNL REVDAT 2 27-JUN-18 5MCW 1 REMARK REVDAT 1 13-JUN-18 5MCW 0 JRNL AUTH D.GOLOVENKO,B.BRAUNING,P.VYAS,T.E.HARAN,H.ROZENBERG, JRNL AUTH 2 Z.SHAKKED JRNL TITL NEW INSIGHTS INTO THE ROLE OF DNA SHAPE ON ITS RECOGNITION JRNL TITL 2 BY P53 PROTEINS. JRNL REF STRUCTURE V. 26 1237 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 30057026 JRNL DOI 10.1016/J.STR.2018.06.006 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV-2276_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 40244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.670 REMARK 3 FREE R VALUE TEST SET COUNT : 3085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8314 - 4.2186 0.96 3676 307 0.1687 0.2016 REMARK 3 2 4.2186 - 3.3486 1.00 3648 297 0.1635 0.1850 REMARK 3 3 3.3486 - 2.9254 1.00 3600 301 0.1878 0.2331 REMARK 3 4 2.9254 - 2.6580 0.99 3570 294 0.2008 0.2294 REMARK 3 5 2.6580 - 2.4675 1.00 3557 299 0.2059 0.2472 REMARK 3 6 2.4675 - 2.3220 0.99 3526 283 0.2089 0.2510 REMARK 3 7 2.3220 - 2.2057 0.97 3470 286 0.2261 0.2968 REMARK 3 8 2.2057 - 2.1097 0.94 3367 285 0.2361 0.2801 REMARK 3 9 2.1097 - 2.0285 0.89 3159 264 0.2379 0.2752 REMARK 3 10 2.0285 - 1.9585 0.83 2946 240 0.2570 0.2723 REMARK 3 11 1.9585 - 1.8972 0.75 2640 229 0.2678 0.2915 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3722 REMARK 3 ANGLE : 0.867 5140 REMARK 3 CHIRALITY : 0.053 558 REMARK 3 PLANARITY : 0.006 611 REMARK 3 DIHEDRAL : 20.614 2189 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 139.2790 81.0226 12.8799 REMARK 3 T TENSOR REMARK 3 T11: 0.1124 T22: 0.2340 REMARK 3 T33: 0.1291 T12: 0.0086 REMARK 3 T13: -0.0281 T23: -0.0530 REMARK 3 L TENSOR REMARK 3 L11: 2.9354 L22: 0.8206 REMARK 3 L33: 0.6497 L12: 0.1360 REMARK 3 L13: 0.7893 L23: -0.3871 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: 0.2056 S13: -0.2935 REMARK 3 S21: 0.0135 S22: 0.2093 S23: -0.2475 REMARK 3 S31: 0.0207 S32: 0.2939 S33: -0.2082 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 124 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 136.8627 75.6028 12.8260 REMARK 3 T TENSOR REMARK 3 T11: 0.1356 T22: 0.1438 REMARK 3 T33: 0.2460 T12: 0.0243 REMARK 3 T13: -0.0385 T23: -0.0665 REMARK 3 L TENSOR REMARK 3 L11: 2.6472 L22: 0.4924 REMARK 3 L33: 0.8219 L12: -0.3551 REMARK 3 L13: 0.4725 L23: -0.4636 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: 0.2261 S13: -0.4364 REMARK 3 S21: 0.0396 S22: 0.0900 S23: -0.2640 REMARK 3 S31: 0.1200 S32: 0.1747 S33: -0.0857 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): 129.2440 89.3781 19.6349 REMARK 3 T TENSOR REMARK 3 T11: 0.1551 T22: 0.0614 REMARK 3 T33: 0.0495 T12: -0.0117 REMARK 3 T13: -0.0490 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.6466 L22: 0.9282 REMARK 3 L33: 0.3624 L12: -0.5421 REMARK 3 L13: 0.1565 L23: -0.2870 REMARK 3 S TENSOR REMARK 3 S11: -0.1256 S12: 0.0064 S13: 0.0070 REMARK 3 S21: 0.1304 S22: 0.1210 S23: -0.0161 REMARK 3 S31: -0.0489 S32: 0.0035 S33: 0.1741 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 177 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 118.6921 78.1699 25.5928 REMARK 3 T TENSOR REMARK 3 T11: 0.1739 T22: 0.1904 REMARK 3 T33: 0.2710 T12: 0.0235 REMARK 3 T13: 0.0075 T23: 0.1262 REMARK 3 L TENSOR REMARK 3 L11: 0.9630 L22: 2.2425 REMARK 3 L33: 4.2848 L12: -0.6960 REMARK 3 L13: 1.3988 L23: 0.9692 REMARK 3 S TENSOR REMARK 3 S11: -0.0846 S12: -0.6236 S13: -0.6444 REMARK 3 S21: 0.3734 S22: 0.0241 S23: 0.2939 REMARK 3 S31: 0.3028 S32: -0.3323 S33: -0.7973 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 131.6929 80.2506 28.6401 REMARK 3 T TENSOR REMARK 3 T11: 0.1731 T22: 0.1313 REMARK 3 T33: 0.2725 T12: 0.0177 REMARK 3 T13: -0.0782 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 1.1830 L22: 2.3748 REMARK 3 L33: 1.7731 L12: -0.8697 REMARK 3 L13: -0.7491 L23: -0.3579 REMARK 3 S TENSOR REMARK 3 S11: 0.0323 S12: -0.0420 S13: -0.0467 REMARK 3 S21: 0.5603 S22: 0.1180 S23: -0.5205 REMARK 3 S31: 0.0784 S32: 0.0466 S33: -0.1291 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 142.6638 70.3670 21.6545 REMARK 3 T TENSOR REMARK 3 T11: 0.1972 T22: 0.2577 REMARK 3 T33: 0.4642 T12: 0.0756 REMARK 3 T13: -0.0874 T23: -0.1241 REMARK 3 L TENSOR REMARK 3 L11: 0.3622 L22: 0.6173 REMARK 3 L33: 0.7086 L12: 0.4680 REMARK 3 L13: -0.2690 L23: -0.4311 REMARK 3 S TENSOR REMARK 3 S11: -0.0584 S12: 0.3274 S13: -0.5969 REMARK 3 S21: -0.0411 S22: -0.0108 S23: -0.2739 REMARK 3 S31: 0.2539 S32: 0.1293 S33: -0.0570 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 230 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 131.7817 82.2770 17.0089 REMARK 3 T TENSOR REMARK 3 T11: 0.0653 T22: 0.1443 REMARK 3 T33: 0.2573 T12: 0.0005 REMARK 3 T13: -0.0496 T23: -0.0392 REMARK 3 L TENSOR REMARK 3 L11: 1.1827 L22: 0.6604 REMARK 3 L33: 0.9327 L12: -0.2425 REMARK 3 L13: 0.3805 L23: -0.2091 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: -0.0379 S13: 0.0591 REMARK 3 S21: 0.0960 S22: 0.0863 S23: -0.0215 REMARK 3 S31: -0.0693 S32: 0.0906 S33: -0.0264 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 292 ) REMARK 3 ORIGIN FOR THE GROUP (A): 128.0065 82.4019 -2.9226 REMARK 3 T TENSOR REMARK 3 T11: 0.1845 T22: 0.3547 REMARK 3 T33: 0.1725 T12: -0.0142 REMARK 3 T13: -0.0066 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 4.0999 L22: 4.7005 REMARK 3 L33: 1.5333 L12: 1.4737 REMARK 3 L13: 0.3581 L23: 0.7402 REMARK 3 S TENSOR REMARK 3 S11: -0.0733 S12: 0.9172 S13: 0.2566 REMARK 3 S21: -0.7158 S22: 0.2642 S23: 0.0679 REMARK 3 S31: -0.0860 S32: 0.1465 S33: -0.1172 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 94 THROUGH 123 ) REMARK 3 ORIGIN FOR THE GROUP (A): 139.2836 46.8289 12.8845 REMARK 3 T TENSOR REMARK 3 T11: 0.1458 T22: 0.1660 REMARK 3 T33: 0.2488 T12: 0.0183 REMARK 3 T13: -0.0006 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 3.2846 L22: 0.7795 REMARK 3 L33: 0.9076 L12: -0.4552 REMARK 3 L13: 0.5647 L23: -0.2877 REMARK 3 S TENSOR REMARK 3 S11: 0.0004 S12: 0.4079 S13: -0.0879 REMARK 3 S21: -0.0896 S22: 0.0828 S23: -0.3512 REMARK 3 S31: -0.0146 S32: 0.2881 S33: -0.1052 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 124 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 132.2974 47.0763 16.1124 REMARK 3 T TENSOR REMARK 3 T11: 0.0968 T22: 0.1379 REMARK 3 T33: 0.1603 T12: 0.0227 REMARK 3 T13: -0.0169 T23: -0.0337 REMARK 3 L TENSOR REMARK 3 L11: 2.1133 L22: 0.7715 REMARK 3 L33: 0.7605 L12: 0.3146 REMARK 3 L13: 0.4224 L23: -0.2129 REMARK 3 S TENSOR REMARK 3 S11: -0.0581 S12: 0.0015 S13: 0.0890 REMARK 3 S21: 0.0662 S22: 0.1714 S23: -0.2532 REMARK 3 S31: 0.0205 S32: 0.1009 S33: -0.0219 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 181 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): 120.0259 42.7891 26.6380 REMARK 3 T TENSOR REMARK 3 T11: 0.2329 T22: 0.2745 REMARK 3 T33: 0.2323 T12: -0.0307 REMARK 3 T13: 0.0281 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 8.5163 L22: 1.6460 REMARK 3 L33: 2.6162 L12: -0.8307 REMARK 3 L13: 0.5003 L23: 1.9630 REMARK 3 S TENSOR REMARK 3 S11: -0.2047 S12: -0.7613 S13: -1.0635 REMARK 3 S21: 0.4209 S22: -0.0049 S23: 0.2540 REMARK 3 S31: 0.6900 S32: -0.7384 S33: -0.1241 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 195 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 131.6916 46.0553 28.6380 REMARK 3 T TENSOR REMARK 3 T11: 0.2019 T22: 0.1109 REMARK 3 T33: 0.0775 T12: 0.0100 REMARK 3 T13: -0.0737 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 0.3502 L22: 2.3655 REMARK 3 L33: 1.0704 L12: -0.0152 REMARK 3 L13: 0.1687 L23: 0.3468 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: -0.1418 S13: -0.0736 REMARK 3 S21: 0.3012 S22: 0.1099 S23: -0.2303 REMARK 3 S31: 0.0781 S32: -0.0120 S33: 0.1731 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 214 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 134.4600 45.0557 18.1482 REMARK 3 T TENSOR REMARK 3 T11: 0.1645 T22: 0.0729 REMARK 3 T33: 0.0457 T12: 0.0300 REMARK 3 T13: -0.0308 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.3890 L22: 0.3726 REMARK 3 L33: 1.1111 L12: 0.4557 REMARK 3 L13: 0.4832 L23: -0.0076 REMARK 3 S TENSOR REMARK 3 S11: -0.0619 S12: 0.1882 S13: -0.1575 REMARK 3 S21: 0.0937 S22: 0.0523 S23: -0.1316 REMARK 3 S31: 0.0927 S32: 0.1064 S33: -0.0755 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 278 THROUGH 292 ) REMARK 3 ORIGIN FOR THE GROUP (A): 128.0052 48.1999 -2.9467 REMARK 3 T TENSOR REMARK 3 T11: 0.1931 T22: 0.3254 REMARK 3 T33: 0.1307 T12: -0.0193 REMARK 3 T13: 0.0146 T23: -0.0283 REMARK 3 L TENSOR REMARK 3 L11: 2.7318 L22: 3.4417 REMARK 3 L33: 1.5002 L12: -0.9426 REMARK 3 L13: 1.4564 L23: 0.9987 REMARK 3 S TENSOR REMARK 3 S11: -0.1053 S12: 0.7565 S13: 0.1993 REMARK 3 S21: -0.5556 S22: 0.1134 S23: -0.3635 REMARK 3 S31: -0.1374 S32: 0.2519 S33: -0.0285 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 111.3144 86.2057 0.1141 REMARK 3 T TENSOR REMARK 3 T11: 0.1977 T22: 0.2187 REMARK 3 T33: 0.0276 T12: -0.0075 REMARK 3 T13: 0.0004 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 0.4388 L22: 0.6789 REMARK 3 L33: 1.3087 L12: -0.3009 REMARK 3 L13: 0.0902 L23: 0.1125 REMARK 3 S TENSOR REMARK 3 S11: 0.0758 S12: 0.1813 S13: -0.0242 REMARK 3 S21: -0.1932 S22: -0.0121 S23: 0.0541 REMARK 3 S31: 0.0840 S32: -0.0444 S33: 0.0605 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 11 THROUGH 20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 111.3217 52.0009 0.1356 REMARK 3 T TENSOR REMARK 3 T11: 0.1586 T22: 0.1641 REMARK 3 T33: 0.3807 T12: -0.0295 REMARK 3 T13: 0.0244 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 2.8716 L22: 2.4363 REMARK 3 L33: 2.4689 L12: -0.5910 REMARK 3 L13: 0.1023 L23: -0.2507 REMARK 3 S TENSOR REMARK 3 S11: 0.1486 S12: 0.2804 S13: 0.0565 REMARK 3 S21: -0.3287 S22: -0.0993 S23: -0.1319 REMARK 3 S31: 0.1017 S32: -0.1698 S33: -0.1030 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TRANSLATIONAL NON-CRYSTALLOGRAPHIC REMARK 3 SYMMETRY (TNCS) CORRECTION REMARK 4 REMARK 4 5MCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002288. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88560 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40479 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.897 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : 0.14300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: 1TSR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M CITRIC ACID, 0.08 M BIS-TRIS REMARK 280 PROPANE, 18% W/V POLYETHYLENE GLYCOL 3,350, PH 8.8, EVAPORATION, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 55.70150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.20400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 55.70150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.20400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 136.81600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 293 REMARK 465 GLY B 293 REMARK 465 DT C 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 LYS A 292 CE NZ REMARK 470 LYS B 291 CG CD CE NZ REMARK 470 LYS B 292 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 126 O HOH C 151 1.70 REMARK 500 O HOH B 547 O HOH B 579 1.78 REMARK 500 OD1 ASP B 184 O HOH B 401 1.87 REMARK 500 OP2 DC C 19 O HOH C 101 1.91 REMARK 500 OP2 DI C 15 O HOH C 102 2.01 REMARK 500 O HOH C 125 O HOH C 157 2.01 REMARK 500 O HOH C 132 O HOH C 137 2.03 REMARK 500 O HOH A 559 O HOH A 588 2.04 REMARK 500 O HOH A 582 O HOH A 618 2.06 REMARK 500 O HOH B 519 O HOH B 581 2.06 REMARK 500 OE1 GLU A 221 O HOH A 401 2.09 REMARK 500 O HOH A 536 O HOH A 584 2.13 REMARK 500 O HOH B 584 O HOH B 604 2.18 REMARK 500 O HOH B 480 O HOH B 592 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 P DG C 1 O3' DC C 20 1565 1.61 REMARK 500 OP1 DG C 1 O3' DC C 20 1565 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 118 10.57 -145.33 REMARK 500 SER A 183 76.42 -69.04 REMARK 500 LEU A 188 -48.06 -133.29 REMARK 500 THR B 118 26.36 -142.54 REMARK 500 ALA B 138 -0.22 67.91 REMARK 500 SER B 183 85.80 -67.65 REMARK 500 ASP B 184 18.51 -143.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 176 SG REMARK 620 2 HIS A 179 ND1 105.4 REMARK 620 3 CYS A 238 SG 111.6 113.9 REMARK 620 4 CYS A 242 SG 113.4 99.9 112.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 176 SG REMARK 620 2 HIS B 179 ND1 105.7 REMARK 620 3 CYS B 238 SG 110.7 109.3 REMARK 620 4 CYS B 242 SG 115.1 100.8 114.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KZ8 RELATED DB: PDB REMARK 900 RELATED ID: 5MCT RELATED DB: PDB REMARK 900 RELATED ID: 5MCU RELATED DB: PDB REMARK 900 RELATED ID: 5MCV RELATED DB: PDB REMARK 900 RELATED ID: 5MG7 RELATED DB: PDB REMARK 900 RELATED ID: 5MF7 RELATED DB: PDB REMARK 900 RELATED ID: 6FJ5 RELATED DB: PDB DBREF 5MCW A 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 5MCW B 94 293 UNP P04637 P53_HUMAN 94 293 DBREF 5MCW C 0 20 PDB 5MCW 5MCW 0 20 SEQRES 1 A 200 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 A 200 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 A 200 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 A 200 MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 A 200 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 A 200 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 A 200 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 A 200 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 A 200 GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP ARG ASN SEQRES 10 A 200 THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO SEQRES 11 A 200 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 A 200 MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 A 200 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 A 200 ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG VAL CYS SEQRES 15 A 200 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 A 200 LEU ARG LYS LYS GLY SEQRES 1 B 200 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER SEQRES 2 B 200 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA SEQRES 3 B 200 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS SEQRES 4 B 200 MET PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU SEQRES 5 B 200 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG SEQRES 6 B 200 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU SEQRES 7 B 200 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP SEQRES 8 B 200 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL SEQRES 9 B 200 GLU GLY ASN LEU ARG VAL GLU TYR LEU ASP ASP ARG ASN SEQRES 10 B 200 THR PHE ARG HIS SER VAL VAL VAL PRO TYR GLU PRO PRO SEQRES 11 B 200 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR SEQRES 12 B 200 MET CYS ASN SER SER CYS MET GLY GLY MET ASN ARG ARG SEQRES 13 B 200 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY SEQRES 14 B 200 ASN LEU LEU GLY ARG ASN SER PHE GLU VAL ARG VAL CYS SEQRES 15 B 200 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN SEQRES 16 B 200 LEU ARG LYS LYS GLY SEQRES 1 C 21 DT DG DG DG DC DI 5CM DG DC DC DC DG DG SEQRES 2 C 21 DG DC DI 5CM DG DC DC DC HET 5CM C 6 20 HET 5CM C 16 20 HET ZN A 301 1 HET FOR A 302 2 HET ZN B 301 1 HET FOR B 302 2 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION HETNAM FOR FORMYL GROUP FORMUL 3 5CM 2(C10 H16 N3 O7 P) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 FOR 2(C H2 O) FORMUL 8 HOH *513(H2 O) HELIX 1 AA1 GLN A 165 MET A 169 5 5 HELIX 2 AA2 CYS A 176 CYS A 182 1 7 HELIX 3 AA3 CYS A 277 LYS A 292 1 16 HELIX 4 AA4 GLN B 165 MET B 169 5 5 HELIX 5 AA5 CYS B 176 CYS B 182 1 7 HELIX 6 AA6 CYS B 277 LYS B 292 1 16 SHEET 1 AA1 4 ARG A 110 GLY A 112 0 SHEET 2 AA1 4 CYS A 141 TRP A 146 -1 O GLN A 144 N GLY A 112 SHEET 3 AA1 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145 SHEET 4 AA1 4 ILE A 195 VAL A 197 -1 N ARG A 196 O ASN A 235 SHEET 1 AA2 7 CYS A 124 SER A 127 0 SHEET 2 AA2 7 LYS A 132 CYS A 135 -1 O PHE A 134 N THR A 125 SHEET 3 AA2 7 LEU A 264 VAL A 274 1 O GLU A 271 N MET A 133 SHEET 4 AA2 7 ILE A 251 GLU A 258 -1 N LEU A 257 O LEU A 265 SHEET 5 AA2 7 ARG A 156 TYR A 163 -1 N MET A 160 O ILE A 254 SHEET 6 AA2 7 HIS A 214 PRO A 219 -1 O VAL A 218 N VAL A 157 SHEET 7 AA2 7 GLU A 204 ASP A 207 -1 N GLU A 204 O VAL A 217 SHEET 1 AA3 4 ARG B 110 GLY B 112 0 SHEET 2 AA3 4 CYS B 141 TRP B 146 -1 O GLN B 144 N GLY B 112 SHEET 3 AA3 4 THR B 230 TYR B 236 -1 O ILE B 232 N VAL B 143 SHEET 4 AA3 4 ILE B 195 VAL B 197 -1 N ARG B 196 O ASN B 235 SHEET 1 AA4 7 CYS B 124 SER B 127 0 SHEET 2 AA4 7 LYS B 132 CYS B 135 -1 O PHE B 134 N THR B 125 SHEET 3 AA4 7 LEU B 264 VAL B 274 1 O GLU B 271 N MET B 133 SHEET 4 AA4 7 ILE B 251 GLU B 258 -1 N LEU B 257 O LEU B 265 SHEET 5 AA4 7 ARG B 156 TYR B 163 -1 N MET B 160 O ILE B 254 SHEET 6 AA4 7 HIS B 214 PRO B 219 -1 O VAL B 218 N VAL B 157 SHEET 7 AA4 7 GLU B 204 ASP B 207 -1 N GLU B 204 O VAL B 217 LINK O3' DI C 5 P 5CM C 6 1555 1555 1.60 LINK O3' 5CM C 6 P DG C 7 1555 1555 1.60 LINK O3' DI C 15 P 5CM C 16 1555 1555 1.61 LINK O3' 5CM C 16 P DG C 17 1555 1555 1.60 LINK SG CYS A 176 ZN ZN A 301 1555 1555 2.32 LINK ND1 HIS A 179 ZN ZN A 301 1555 1555 2.02 LINK SG CYS A 238 ZN ZN A 301 1555 1555 2.32 LINK SG CYS A 242 ZN ZN A 301 1555 1555 2.28 LINK SG CYS B 176 ZN ZN B 301 1555 1555 2.32 LINK ND1 HIS B 179 ZN ZN B 301 1555 1555 2.02 LINK SG CYS B 238 ZN ZN B 301 1555 1555 2.40 LINK SG CYS B 242 ZN ZN B 301 1555 1555 2.33 SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242 SITE 1 AC2 4 CYS B 176 HIS B 179 CYS B 238 CYS B 242 CRYST1 111.403 68.408 69.680 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014351 0.00000