PDB Short entry for 5CL5 HEADER HYDROLASE/DNA 16-JUL-15 5CL5 TITLE ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A 3- TITLE 2 METHYLADENINE ANALOG OR DNA CONTAINING AN ABASIC SITE AND A FREE TITLE 3 NUCLEOBASE (51% SUBSTRATE/49% PRODUCT AT 48 HOURS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKD; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: SEE SEQUENCE DETAILS; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 ATCC: 14579; SOURCE 5 GENE: IKE_03968; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBG103; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS DNA GLYCOSYLASE, HEAT-LIKE REPEAT, PROTEIN-DNA COMPLEX, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.A.MULLINS,B.F.EICHMAN REVDAT 6 27-SEP-23 5CL5 1 REMARK REVDAT 5 27-NOV-19 5CL5 1 REMARK REVDAT 4 13-SEP-17 5CL5 1 JRNL REMARK REVDAT 3 25-NOV-15 5CL5 1 JRNL REVDAT 2 18-NOV-15 5CL5 1 JRNL REVDAT 1 28-OCT-15 5CL5 0 JRNL AUTH E.A.MULLINS,R.SHI,Z.D.PARSONS,P.K.YUEN,S.S.DAVID,Y.IGARASHI, JRNL AUTH 2 B.F.EICHMAN JRNL TITL THE DNA GLYCOSYLASE ALKD USES A NON-BASE-FLIPPING MECHANISM JRNL TITL 2 TO EXCISE BULKY LESIONS. JRNL REF NATURE V. 527 254 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26524531 JRNL DOI 10.1038/NATURE15728 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 43431 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 2016 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 35.3419 - 3.7811 0.99 3000 149 0.1385 0.1685 REMARK 3 2 3.7811 - 3.0017 1.00 2976 146 0.1476 0.1748 REMARK 3 3 3.0017 - 2.6224 1.00 2990 146 0.1666 0.1880 REMARK 3 4 2.6224 - 2.3827 1.00 2957 142 0.1681 0.1858 REMARK 3 5 2.3827 - 2.2119 1.00 2965 142 0.1560 0.2216 REMARK 3 6 2.2119 - 2.0815 1.00 2979 144 0.1508 0.1733 REMARK 3 7 2.0815 - 1.9773 1.00 2947 146 0.1650 0.2020 REMARK 3 8 1.9773 - 1.8912 1.00 2967 148 0.1613 0.1715 REMARK 3 9 1.8912 - 1.8184 1.00 2950 136 0.1626 0.2318 REMARK 3 10 1.8184 - 1.7557 1.00 2964 147 0.1658 0.2004 REMARK 3 11 1.7557 - 1.7008 1.00 2958 144 0.1724 0.2331 REMARK 3 12 1.7008 - 1.6522 1.00 2953 144 0.1796 0.1911 REMARK 3 13 1.6522 - 1.6087 1.00 2937 144 0.1867 0.2255 REMARK 3 14 1.6087 - 1.5694 0.97 2872 138 0.2076 0.2378 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.13 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 2646 REMARK 3 ANGLE : 1.052 3709 REMARK 3 CHIRALITY : 0.045 400 REMARK 3 PLANARITY : 0.006 375 REMARK 3 DIHEDRAL : 18.761 1022 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.0146 21.0868 21.3771 REMARK 3 T TENSOR REMARK 3 T11: 0.2122 T22: 0.1194 REMARK 3 T33: 0.1669 T12: -0.0153 REMARK 3 T13: 0.0299 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.5654 L22: 5.7227 REMARK 3 L33: 5.7144 L12: -1.5672 REMARK 3 L13: 0.6429 L23: -5.1033 REMARK 3 S TENSOR REMARK 3 S11: 0.0515 S12: 0.0402 S13: 0.3223 REMARK 3 S21: 0.2355 S22: -0.1563 S23: -0.1289 REMARK 3 S31: -0.5924 S32: 0.1147 S33: 0.0526 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.3085 7.0264 26.2207 REMARK 3 T TENSOR REMARK 3 T11: 0.1084 T22: 0.1301 REMARK 3 T33: 0.0949 T12: 0.0071 REMARK 3 T13: -0.0183 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 3.4896 L22: 2.1693 REMARK 3 L33: 5.4984 L12: -0.2908 REMARK 3 L13: -3.0419 L23: 1.2446 REMARK 3 S TENSOR REMARK 3 S11: -0.1011 S12: -0.2721 S13: -0.0941 REMARK 3 S21: 0.1300 S22: 0.0752 S23: -0.1016 REMARK 3 S31: 0.1744 S32: 0.4044 S33: 0.0333 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.2786 12.9279 17.8428 REMARK 3 T TENSOR REMARK 3 T11: 0.0999 T22: 0.1145 REMARK 3 T33: 0.1084 T12: -0.0081 REMARK 3 T13: -0.0149 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 3.4509 L22: 4.5959 REMARK 3 L33: 4.8735 L12: -1.0207 REMARK 3 L13: 0.9333 L23: -2.5130 REMARK 3 S TENSOR REMARK 3 S11: 0.1165 S12: 0.0892 S13: 0.0466 REMARK 3 S21: -0.0856 S22: 0.0808 S23: 0.3805 REMARK 3 S31: -0.0416 S32: -0.2826 S33: -0.1917 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.9143 20.4460 11.3356 REMARK 3 T TENSOR REMARK 3 T11: 0.1467 T22: 0.0733 REMARK 3 T33: 0.1060 T12: -0.0061 REMARK 3 T13: 0.0250 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 3.8656 L22: 4.1857 REMARK 3 L33: 7.0518 L12: -1.6895 REMARK 3 L13: 3.6117 L23: -3.0629 REMARK 3 S TENSOR REMARK 3 S11: -0.0961 S12: 0.1018 S13: 0.2850 REMARK 3 S21: 0.0632 S22: -0.0574 S23: -0.0343 REMARK 3 S31: -0.4704 S32: 0.1358 S33: 0.1640 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 73.8706 10.3832 2.7257 REMARK 3 T TENSOR REMARK 3 T11: 0.1239 T22: 0.0943 REMARK 3 T33: 0.0994 T12: -0.0134 REMARK 3 T13: -0.0001 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.5575 L22: 0.6801 REMARK 3 L33: 2.5640 L12: -0.2848 REMARK 3 L13: -0.7368 L23: 0.3800 REMARK 3 S TENSOR REMARK 3 S11: 0.0310 S12: 0.0442 S13: 0.0267 REMARK 3 S21: -0.0547 S22: 0.0076 S23: 0.0202 REMARK 3 S31: -0.0755 S32: -0.1130 S33: -0.0305 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.5484 0.1496 -1.1692 REMARK 3 T TENSOR REMARK 3 T11: 0.0836 T22: 0.0562 REMARK 3 T33: 0.0617 T12: -0.0123 REMARK 3 T13: -0.0063 T23: 0.0199 REMARK 3 L TENSOR REMARK 3 L11: 3.2081 L22: 3.6817 REMARK 3 L33: 4.2297 L12: 0.5427 REMARK 3 L13: 0.5249 L23: 1.7468 REMARK 3 S TENSOR REMARK 3 S11: 0.0172 S12: 0.0342 S13: -0.1276 REMARK 3 S21: -0.1646 S22: 0.0012 S23: 0.1606 REMARK 3 S31: 0.1307 S32: -0.1265 S33: -0.0171 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): 87.9583 -1.9143 -3.3113 REMARK 3 T TENSOR REMARK 3 T11: 0.1091 T22: 0.0492 REMARK 3 T33: 0.0701 T12: 0.0052 REMARK 3 T13: 0.0095 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 3.9633 L22: 2.6007 REMARK 3 L33: 3.8564 L12: 0.5643 REMARK 3 L13: 0.2287 L23: 0.6588 REMARK 3 S TENSOR REMARK 3 S11: 0.0627 S12: 0.1933 S13: -0.1084 REMARK 3 S21: -0.2166 S22: 0.0493 S23: -0.0538 REMARK 3 S31: 0.0756 S32: 0.2449 S33: -0.1173 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.7219 -13.1321 1.6570 REMARK 3 T TENSOR REMARK 3 T11: 0.1413 T22: 0.0840 REMARK 3 T33: 0.0967 T12: -0.0099 REMARK 3 T13: 0.0140 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.9673 L22: 3.7344 REMARK 3 L33: 1.0165 L12: 0.0238 REMARK 3 L13: -0.0955 L23: 1.0426 REMARK 3 S TENSOR REMARK 3 S11: -0.0412 S12: -0.0127 S13: -0.1477 REMARK 3 S21: -0.0221 S22: 0.0078 S23: 0.0274 REMARK 3 S31: 0.1783 S32: -0.0219 S33: 0.0325 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.3829 -9.7591 18.3760 REMARK 3 T TENSOR REMARK 3 T11: 0.1690 T22: 0.2563 REMARK 3 T33: 0.2654 T12: 0.0302 REMARK 3 T13: 0.0491 T23: 0.0867 REMARK 3 L TENSOR REMARK 3 L11: 0.0954 L22: 2.4722 REMARK 3 L33: 1.9830 L12: -0.2897 REMARK 3 L13: -0.3781 L23: 0.3911 REMARK 3 S TENSOR REMARK 3 S11: -0.2817 S12: -0.5338 S13: -0.5595 REMARK 3 S21: 0.1019 S22: 0.1513 S23: -0.0029 REMARK 3 S31: 0.1875 S32: -0.1350 S33: -0.0163 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 84.4363 -14.1039 20.0028 REMARK 3 T TENSOR REMARK 3 T11: 0.1474 T22: 0.5657 REMARK 3 T33: 0.5772 T12: 0.0498 REMARK 3 T13: 0.0834 T23: 0.2817 REMARK 3 L TENSOR REMARK 3 L11: 6.7457 L22: 1.8076 REMARK 3 L33: 0.4844 L12: -0.5523 REMARK 3 L13: -1.0854 L23: 0.8211 REMARK 3 S TENSOR REMARK 3 S11: -0.2986 S12: 0.2979 S13: -0.7629 REMARK 3 S21: 0.1721 S22: 0.1639 S23: 0.1119 REMARK 3 S31: 0.1717 S32: 0.1513 S33: 0.0740 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.2801 -5.9504 17.7862 REMARK 3 T TENSOR REMARK 3 T11: 0.2006 T22: 0.2970 REMARK 3 T33: 0.2811 T12: 0.0676 REMARK 3 T13: -0.0144 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 6.6213 L22: 6.0995 REMARK 3 L33: 4.4282 L12: 2.6825 REMARK 3 L13: -0.8456 L23: 0.6391 REMARK 3 S TENSOR REMARK 3 S11: -0.2927 S12: -0.0822 S13: -0.6881 REMARK 3 S21: -0.3240 S22: 0.3230 S23: 0.7023 REMARK 3 S31: -0.4874 S32: -0.7665 S33: -0.0075 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43466 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.569 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.42200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.133 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3BVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% W/V PEG4000, 42 MM SODIUM ACETATE, REMARK 280 PH 4.6, 85 MM AMMONIUM ACETATE, 5% V/V GLYCEROL, PH 5.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 46.70000 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 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 -3 REMARK 465 PRO A -2 REMARK 465 GLU A 230 REMARK 465 LYS A 231 REMARK 465 ILE A 232 REMARK 465 GLY A 233 REMARK 465 GLU A 234 REMARK 465 THR A 235 REMARK 465 LEU A 236 REMARK 465 SER A 237 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 106 O HOH C 118 2.10 REMARK 500 O HOH A 455 O HOH A 479 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 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 17 O4' - C1' - N1 ANGL. DEV. = 2.0 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 54 152.76 69.70 REMARK 500 THR A 118 -69.68 -98.06 REMARK 500 TYR A 134 -44.93 -132.26 REMARK 500 LYS A 158 -120.99 51.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 609 DISTANCE = 5.96 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 54K B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CL3 RELATED DB: PDB REMARK 900 RELATED ID: 5CL4 RELATED DB: PDB REMARK 900 RELATED ID: 5CL6 RELATED DB: PDB REMARK 900 RELATED ID: 5CL7 RELATED DB: PDB REMARK 900 RELATED ID: 5CL8 RELATED DB: PDB REMARK 900 RELATED ID: 5CL9 RELATED DB: PDB REMARK 900 RELATED ID: 5CLA RELATED DB: PDB REMARK 900 RELATED ID: 5CLB RELATED DB: PDB REMARK 900 RELATED ID: 5CLC RELATED DB: PDB REMARK 900 RELATED ID: 5CLD RELATED DB: PDB REMARK 900 RELATED ID: 5CLE RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAIN B CONTAINS MICROHETEROGENEITY AT POSITION 6 (DZM VERSUS ORP). DBREF 5CL5 A 1 237 UNP R8GWR7 R8GWR7_BACCE 1 237 DBREF 5CL5 B 1 12 PDB 5CL5 5CL5 1 12 DBREF 5CL5 C 13 24 PDB 5CL5 5CL5 13 24 SEQADV 5CL5 GLY A -3 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL5 PRO A -2 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL5 VAL A -1 UNP R8GWR7 EXPRESSION TAG SEQADV 5CL5 PRO A 0 UNP R8GWR7 EXPRESSION TAG SEQRES 1 A 241 GLY PRO VAL PRO MET HIS PRO PHE VAL LYS ALA LEU GLN SEQRES 2 A 241 GLU HIS PHE THR ALA HIS GLN ASN PRO GLU LYS ALA GLU SEQRES 3 A 241 PRO MET ALA ARG TYR MET LYS ASN HIS PHE LEU PHE LEU SEQRES 4 A 241 GLY ILE GLN THR PRO GLU ARG ARG GLN LEU LEU LYS ASP SEQRES 5 A 241 ILE ILE GLN ILE HIS THR LEU PRO ASP GLN LYS ASP PHE SEQRES 6 A 241 GLN ILE ILE ILE ARG GLU LEU TRP ASP LEU PRO GLU ARG SEQRES 7 A 241 GLU PHE GLN ALA ALA ALA LEU ASP ILE MET GLN LYS TYR SEQRES 8 A 241 LYS LYS HIS ILE ASN GLU THR HIS ILE PRO PHE LEU GLU SEQRES 9 A 241 GLU LEU ILE VAL THR LYS SER TRP TRP ASP SER VAL ASP SEQRES 10 A 241 SER ILE VAL PRO THR PHE LEU GLY ASP ILE PHE LEU LYS SEQRES 11 A 241 HIS PRO GLU LEU ILE SER ALA TYR ILE PRO LYS TRP ILE SEQRES 12 A 241 ALA SER ASP ASN ILE TRP LEU GLN ARG ALA ALA ILE LEU SEQRES 13 A 241 PHE GLN LEU LYS TYR LYS GLN LYS MET ASP GLU GLU LEU SEQRES 14 A 241 LEU PHE TRP ILE ILE GLY GLN LEU HIS SER SER LYS GLU SEQRES 15 A 241 PHE PHE ILE GLN LYS ALA ILE GLY TRP VAL LEU ARG GLU SEQRES 16 A 241 TYR ALA LYS THR ASN PRO ASP VAL VAL TRP GLU TYR VAL SEQRES 17 A 241 GLN ASN ASN GLU LEU ALA PRO LEU SER LYS ARG GLU ALA SEQRES 18 A 241 ILE LYS HIS ILE LYS GLN ASN TYR GLY ILE ASN ASN GLU SEQRES 19 A 241 LYS ILE GLY GLU THR LEU SER SEQRES 1 B 12 DC DC DC DG DA DZM DA DG DT DC DC DG SEQRES 1 C 12 DC DG DG DA DC DT DT DT DC DG DG DG HET DZM B 6 22 HET ORP B 6 12 HET 54K B 101 11 HETNAM DZM 3-DEAZA-3-METHYLADENINE HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE HETNAM 54K 7-METHYL-3H-IMIDAZO[4,5-C]PYRIDIN-4-AMINE HETSYN DZM 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETSYN 2 DZM PENTOFURANOSYL)-7-METHYL-1H-IMIDAZO[4,5-C]PYRIDIN-4- HETSYN 3 DZM AMINE HETSYN 54K 3-DEAZA-3-METHYLADENINE FORMUL 2 DZM C12 H17 N4 O6 P FORMUL 2 ORP C5 H11 O7 P FORMUL 4 54K C7 H8 N4 FORMUL 5 HOH *356(H2 O) HELIX 1 AA1 HIS A 2 ALA A 14 1 13 HELIX 2 AA2 ASN A 17 MET A 28 1 12 HELIX 3 AA3 GLN A 38 THR A 54 1 17 HELIX 4 AA4 ASP A 57 LYS A 59 5 3 HELIX 5 AA5 ASP A 60 ASP A 70 1 11 HELIX 6 AA6 GLU A 73 TYR A 87 1 15 HELIX 7 AA7 LYS A 88 ILE A 91 5 4 HELIX 8 AA8 ASN A 92 THR A 94 5 3 HELIX 9 AA9 HIS A 95 VAL A 104 1 10 HELIX 10 AB1 TRP A 108 VAL A 116 1 9 HELIX 11 AB2 THR A 118 HIS A 127 1 10 HELIX 12 AB3 PRO A 128 ALA A 133 5 6 HELIX 13 AB4 TYR A 134 SER A 141 1 8 HELIX 14 AB5 ASN A 143 PHE A 153 1 11 HELIX 15 AB6 TYR A 157 MET A 161 5 5 HELIX 16 AB7 ASP A 162 HIS A 174 1 13 HELIX 17 AB8 GLU A 178 ALA A 193 1 16 HELIX 18 AB9 ASN A 196 ASN A 207 1 12 HELIX 19 AC1 ALA A 210 ILE A 218 1 9 HELIX 20 AC2 ILE A 221 GLY A 226 1 6 LINK O3' DA B 5 P ADZM B 6 1555 1555 1.61 LINK O3' DA B 5 P BORP B 6 1555 1555 1.61 LINK O3'ADZM B 6 P DA B 7 1555 1555 1.61 LINK O3 BORP B 6 P DA B 7 1555 1555 1.61 SITE 1 AC1 7 TYR A 27 DA B 5 DA B 7 HOH B 207 SITE 2 AC1 7 DT C 18 DT C 19 DT C 20 CRYST1 38.341 93.400 48.117 90.00 112.85 90.00 P 1 21 1 2 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 0.026082 0.000000 0.010989 0.00000 SCALE2 0.000000 0.010707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022552 0.00000