PDB Short entry for 6P0D HEADER LIGASE 16-MAY-19 6P0D TITLE HUMAN DNA LIGASE 1 (E346A/E592A) BOUND TO AN ADENYLATED, HYDROXYL TITLE 2 TERMINATED DNA NICK COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA LIGASE I,POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] 1; COMPND 5 EC: 6.5.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'- COMPND 18 D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 19 CHAIN: D; COMPND 20 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: LIG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7; 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; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, PHOSPHOTRANSFERASE, OB FOLD, DNA BINDING DOMAIN, KEYWDS 2 ADENYLATION DOMAIN, METALLOENZYME, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.SCHELLENBERG,R.S.WILLIAMS,P.S.TUMBALE,A.A.RICCIO REVDAT 2 11-OCT-23 6P0D 1 REMARK REVDAT 1 11-DEC-19 6P0D 0 JRNL AUTH P.P.TUMBALE,T.J.JURKIW,M.J.SCHELLENBERG,A.A.RICCIO, JRNL AUTH 2 P.J.O'BRIEN,R.S.WILLIAMS JRNL TITL TWO-TIERED ENFORCEMENT OF HIGH-FIDELITY DNA LIGATION. JRNL REF NAT COMMUN V. 10 5431 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31780661 JRNL DOI 10.1038/S41467-019-13478-7 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 86108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 4327 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 34.2823 - 5.3969 0.97 2895 146 0.1644 0.1726 REMARK 3 2 5.3969 - 4.2863 0.99 2772 174 0.1274 0.1471 REMARK 3 3 4.2863 - 3.7452 0.99 2790 151 0.1294 0.1532 REMARK 3 4 3.7452 - 3.4031 1.00 2790 149 0.1360 0.1357 REMARK 3 5 3.4031 - 3.1594 0.99 2756 153 0.1451 0.1556 REMARK 3 6 3.1594 - 2.9732 1.00 2765 134 0.1637 0.1608 REMARK 3 7 2.9732 - 2.8244 1.00 2752 168 0.1611 0.1867 REMARK 3 8 2.8244 - 2.7015 1.00 2773 143 0.1551 0.1857 REMARK 3 9 2.7015 - 2.5976 1.00 2757 131 0.1562 0.1612 REMARK 3 10 2.5976 - 2.5079 1.00 2767 146 0.1554 0.1985 REMARK 3 11 2.5079 - 2.4296 1.00 2740 161 0.1609 0.1862 REMARK 3 12 2.4296 - 2.3601 1.00 2711 150 0.1565 0.1968 REMARK 3 13 2.3601 - 2.2980 1.00 2741 144 0.1553 0.1670 REMARK 3 14 2.2980 - 2.2419 1.00 2776 116 0.1529 0.1968 REMARK 3 15 2.2419 - 2.1910 1.00 2732 133 0.1572 0.1922 REMARK 3 16 2.1910 - 2.1444 1.00 2739 145 0.1655 0.1908 REMARK 3 17 2.1444 - 2.1015 1.00 2726 144 0.1616 0.2131 REMARK 3 18 2.1015 - 2.0618 1.00 2735 150 0.1682 0.1890 REMARK 3 19 2.0618 - 2.0250 1.00 2750 140 0.1736 0.1866 REMARK 3 20 2.0250 - 1.9907 1.00 2730 146 0.1910 0.2377 REMARK 3 21 1.9907 - 1.9586 1.00 2724 146 0.1926 0.2240 REMARK 3 22 1.9586 - 1.9285 1.00 2732 144 0.1967 0.2524 REMARK 3 23 1.9285 - 1.9001 1.00 2714 142 0.2032 0.2311 REMARK 3 24 1.9001 - 1.8733 1.00 2727 142 0.2056 0.2152 REMARK 3 25 1.8733 - 1.8480 1.00 2709 144 0.2164 0.2382 REMARK 3 26 1.8480 - 1.8240 1.00 2727 144 0.2254 0.2750 REMARK 3 27 1.8240 - 1.8012 1.00 2698 144 0.2507 0.2757 REMARK 3 28 1.8012 - 1.7795 0.99 2706 146 0.2627 0.3011 REMARK 3 29 1.7795 - 1.7588 1.00 2718 143 0.2751 0.2586 REMARK 3 30 1.7588 - 1.7500 0.78 2129 108 0.3049 0.3046 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 6155 REMARK 3 ANGLE : 0.706 8535 REMARK 3 CHIRALITY : 0.045 965 REMARK 3 PLANARITY : 0.004 976 REMARK 3 DIHEDRAL : 16.393 3688 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 385 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.9493 12.0831 -11.1028 REMARK 3 T TENSOR REMARK 3 T11: 0.1766 T22: 0.1659 REMARK 3 T33: 0.2383 T12: -0.0109 REMARK 3 T13: 0.0057 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 1.6589 L22: 1.0342 REMARK 3 L33: 1.9744 L12: 0.1865 REMARK 3 L13: -0.4236 L23: 0.0330 REMARK 3 S TENSOR REMARK 3 S11: 0.0830 S12: -0.0770 S13: 0.2907 REMARK 3 S21: 0.0493 S22: -0.0139 S23: 0.0177 REMARK 3 S31: -0.1681 S32: -0.0424 S33: -0.0984 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 386 THROUGH 544 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.5736 2.6221 -13.9962 REMARK 3 T TENSOR REMARK 3 T11: 0.1406 T22: 0.1835 REMARK 3 T33: 0.2076 T12: -0.0002 REMARK 3 T13: -0.0007 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.9555 L22: 1.0258 REMARK 3 L33: 1.2698 L12: 0.3233 REMARK 3 L13: -0.2872 L23: -0.1391 REMARK 3 S TENSOR REMARK 3 S11: -0.0199 S12: -0.0477 S13: 0.0565 REMARK 3 S21: 0.0413 S22: 0.0036 S23: -0.0986 REMARK 3 S31: 0.0026 S32: 0.1146 S33: 0.0061 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 545 THROUGH 741 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1270 -22.5957 -16.2667 REMARK 3 T TENSOR REMARK 3 T11: 0.1826 T22: 0.1425 REMARK 3 T33: 0.1611 T12: 0.0009 REMARK 3 T13: 0.0124 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.6175 L22: 1.6866 REMARK 3 L33: 1.8261 L12: -0.4584 REMARK 3 L13: -0.1787 L23: 0.4795 REMARK 3 S TENSOR REMARK 3 S11: -0.0512 S12: 0.0526 S13: -0.0722 REMARK 3 S21: -0.0393 S22: 0.0046 S23: 0.1060 REMARK 3 S31: 0.0431 S32: -0.1686 S33: 0.0434 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 742 THROUGH 901 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0542 2.4925 -6.7227 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.1848 REMARK 3 T33: 0.2097 T12: 0.0168 REMARK 3 T13: 0.0101 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 2.0206 L22: 1.8252 REMARK 3 L33: 1.5962 L12: -0.3125 REMARK 3 L13: -0.6050 L23: 0.3368 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: -0.0269 S13: 0.1549 REMARK 3 S21: 0.1305 S22: -0.0226 S23: 0.3104 REMARK 3 S31: -0.0255 S32: -0.1990 S33: 0.0111 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.5588 -5.3563 5.5426 REMARK 3 T TENSOR REMARK 3 T11: 0.3118 T22: 0.3215 REMARK 3 T33: 0.2383 T12: 0.0573 REMARK 3 T13: 0.0323 T23: -0.0471 REMARK 3 L TENSOR REMARK 3 L11: 0.3625 L22: 0.1619 REMARK 3 L33: 5.6052 L12: 0.2067 REMARK 3 L13: 1.2804 L23: 0.9488 REMARK 3 S TENSOR REMARK 3 S11: 0.2710 S12: -0.2070 S13: 0.0664 REMARK 3 S21: 0.1111 S22: 0.2394 S23: -0.2460 REMARK 3 S31: -0.3018 S32: -0.1812 S33: -0.4946 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7700 2.8737 -21.0801 REMARK 3 T TENSOR REMARK 3 T11: 0.1647 T22: 0.2180 REMARK 3 T33: 0.1770 T12: 0.0137 REMARK 3 T13: -0.0016 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 3.0331 L22: 1.6156 REMARK 3 L33: 3.8765 L12: 0.9947 REMARK 3 L13: -1.3625 L23: -0.9155 REMARK 3 S TENSOR REMARK 3 S11: -0.0192 S12: 0.2518 S13: 0.1491 REMARK 3 S21: -0.0611 S22: 0.0800 S23: 0.0509 REMARK 3 S31: 0.0642 S32: 0.1479 S33: -0.0599 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 9 THROUGH 18 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2620 0.6737 -15.0712 REMARK 3 T TENSOR REMARK 3 T11: 0.1591 T22: 0.1896 REMARK 3 T33: 0.1726 T12: 0.0163 REMARK 3 T13: -0.0192 T23: -0.0013 REMARK 3 L TENSOR REMARK 3 L11: 2.0171 L22: 1.0407 REMARK 3 L33: 2.8266 L12: 0.6958 REMARK 3 L13: -1.9370 L23: -0.8914 REMARK 3 S TENSOR REMARK 3 S11: 0.0344 S12: 0.0491 S13: 0.1557 REMARK 3 S21: -0.0451 S22: 0.1190 S23: 0.1175 REMARK 3 S31: 0.1270 S32: 0.0322 S33: -0.1409 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 19 THROUGH 23 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9116 -8.2292 7.3495 REMARK 3 T TENSOR REMARK 3 T11: 0.3730 T22: 0.3296 REMARK 3 T33: 0.1825 T12: 0.0362 REMARK 3 T13: 0.0222 T23: -0.0391 REMARK 3 L TENSOR REMARK 3 L11: 0.0969 L22: 3.0795 REMARK 3 L33: 2.5457 L12: 0.4445 REMARK 3 L13: -0.0161 L23: 1.0986 REMARK 3 S TENSOR REMARK 3 S11: 0.0527 S12: -0.0453 S13: -0.0179 REMARK 3 S21: 0.0129 S22: 0.2274 S23: -0.2923 REMARK 3 S31: -0.5394 S32: 0.2269 S33: -0.2018 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 24 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5506 1.5274 19.6013 REMARK 3 T TENSOR REMARK 3 T11: 0.3979 T22: 0.3647 REMARK 3 T33: 0.2475 T12: 0.0579 REMARK 3 T13: 0.0142 T23: -0.0405 REMARK 3 L TENSOR REMARK 3 L11: 3.7592 L22: 6.6921 REMARK 3 L33: 4.1538 L12: 0.7737 REMARK 3 L13: 0.3521 L23: -1.3773 REMARK 3 S TENSOR REMARK 3 S11: 0.0554 S12: -0.1284 S13: 0.4966 REMARK 3 S21: -0.4117 S22: 0.2505 S23: 0.1010 REMARK 3 S31: -0.2620 S32: -0.3598 S33: -0.2387 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 6P0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86232 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 1.01600 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: PHENIX REMARK 200 STARTING MODEL: 1X9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 100 MM LITHIUM ACETATE, REMARK 280 15% (W/V) PEG 3350, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 35.89650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.68400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.61350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.68400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.89650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.61350 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 260 REMARK 465 GLN A 902 REMARK 465 ILE A 903 REMARK 465 GLN A 904 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 HH22 ARG A 589 O HOH A 1104 1.42 REMARK 500 HE ARG A 604 O HOH A 1111 1.52 REMARK 500 OD2 ASP A 827 HH12 ARG A 859 1.53 REMARK 500 HZ3 LYS A 744 O1P AMP C 101 1.53 REMARK 500 HH22 ARG A 898 O HOH A 1116 1.57 REMARK 500 HH11 ARG A 444 O HOH A 1103 1.57 REMARK 500 H GLY A 350 O HOH B 101 1.59 REMARK 500 HZ2 LYS A 642 O HOH A 1131 1.59 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 B 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 13 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC D 26 O4' - C1' - N1 ANGL. DEV. = 2.6 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 HIS A 436 -123.89 56.39 REMARK 500 ALA A 455 -148.51 -138.14 REMARK 500 ARG A 549 32.94 -97.07 REMARK 500 GLU A 559 -116.70 54.64 REMARK 500 ASP A 570 79.54 -104.69 REMARK 500 LYS A 644 -125.41 62.57 REMARK 500 GLU A 692 -51.50 -131.27 REMARK 500 HIS A 740 63.41 -106.63 REMARK 500 ASP A 827 -119.65 47.62 REMARK 500 SER A 839 -52.69 -158.78 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 A1876 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A1877 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH B 146 DISTANCE = 7.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP C 101 DBREF 6P0D A 262 904 UNP P18858 DNLI1_HUMAN 262 904 DBREF 6P0D B 3 13 PDB 6P0D 6P0D 3 13 DBREF 6P0D C 1 7 PDB 6P0D 6P0D 1 7 DBREF 6P0D D 9 26 PDB 6P0D 6P0D 9 26 SEQADV 6P0D SER A 260 UNP P18858 EXPRESSION TAG SEQADV 6P0D ASN A 261 UNP P18858 EXPRESSION TAG SEQADV 6P0D ALA A 346 UNP P18858 GLU 346 ENGINEERED MUTATION SEQADV 6P0D ALA A 592 UNP P18858 GLU 592 ENGINEERED MUTATION SEQRES 1 A 645 SER ASN ASP PRO SER GLY TYR ASN PRO ALA LYS ASN ASN SEQRES 2 A 645 TYR HIS PRO VAL GLU ASP ALA CYS TRP LYS PRO GLY GLN SEQRES 3 A 645 LYS VAL PRO TYR LEU ALA VAL ALA ARG THR PHE GLU LYS SEQRES 4 A 645 ILE GLU GLU VAL SER ALA ARG LEU ARG MET VAL GLU THR SEQRES 5 A 645 LEU SER ASN LEU LEU ARG SER VAL VAL ALA LEU SER PRO SEQRES 6 A 645 PRO ASP LEU LEU PRO VAL LEU TYR LEU SER LEU ASN HIS SEQRES 7 A 645 LEU GLY PRO PRO GLN GLN GLY LEU ALA LEU GLY VAL GLY SEQRES 8 A 645 ASP GLY VAL LEU LEU LYS ALA VAL ALA GLN ALA THR GLY SEQRES 9 A 645 ARG GLN LEU GLU SER VAL ARG ALA GLU ALA ALA GLU LYS SEQRES 10 A 645 GLY ASP VAL GLY LEU VAL ALA GLU ASN SER ARG SER THR SEQRES 11 A 645 GLN ARG LEU MET LEU PRO PRO PRO PRO LEU THR ALA SER SEQRES 12 A 645 GLY VAL PHE SER LYS PHE ARG ASP ILE ALA ARG LEU THR SEQRES 13 A 645 GLY SER ALA SER THR ALA LYS LYS ILE ASP ILE ILE LYS SEQRES 14 A 645 GLY LEU PHE VAL ALA CYS ARG HIS SER GLU ALA ARG PHE SEQRES 15 A 645 ILE ALA ARG SER LEU SER GLY ARG LEU ARG LEU GLY LEU SEQRES 16 A 645 ALA GLU GLN SER VAL LEU ALA ALA LEU SER GLN ALA VAL SEQRES 17 A 645 SER LEU THR PRO PRO GLY GLN GLU PHE PRO PRO ALA MET SEQRES 18 A 645 VAL ASP ALA GLY LYS GLY LYS THR ALA GLU ALA ARG LYS SEQRES 19 A 645 THR TRP LEU GLU GLU GLN GLY MET ILE LEU LYS GLN THR SEQRES 20 A 645 PHE CYS GLU VAL PRO ASP LEU ASP ARG ILE ILE PRO VAL SEQRES 21 A 645 LEU LEU GLU HIS GLY LEU GLU ARG LEU PRO GLU HIS CYS SEQRES 22 A 645 LYS LEU SER PRO GLY ILE PRO LEU LYS PRO MET LEU ALA SEQRES 23 A 645 HIS PRO THR ARG GLY ILE SER GLU VAL LEU LYS ARG PHE SEQRES 24 A 645 GLU GLU ALA ALA PHE THR CYS GLU TYR LYS TYR ASP GLY SEQRES 25 A 645 GLN ARG ALA GLN ILE HIS ALA LEU GLU GLY GLY GLU VAL SEQRES 26 A 645 LYS ILE PHE SER ARG ASN GLN ALA ASP ASN THR GLY LYS SEQRES 27 A 645 TYR PRO ASP ILE ILE SER ARG ILE PRO LYS ILE LYS LEU SEQRES 28 A 645 PRO SER VAL THR SER PHE ILE LEU ASP THR GLU ALA VAL SEQRES 29 A 645 ALA TRP ASP ARG GLU LYS LYS GLN ILE GLN PRO PHE GLN SEQRES 30 A 645 VAL LEU THR THR ARG LYS ARG LYS GLU VAL ASP ALA SER SEQRES 31 A 645 GLU ILE GLN VAL GLN VAL CYS LEU TYR ALA PHE ASP LEU SEQRES 32 A 645 ILE TYR LEU ASN GLY GLU SER LEU VAL ARG GLU PRO LEU SEQRES 33 A 645 SER ARG ARG ARG GLN LEU LEU ARG GLU ASN PHE VAL GLU SEQRES 34 A 645 THR GLU GLY GLU PHE VAL PHE ALA THR SER LEU ASP THR SEQRES 35 A 645 LYS ASP ILE GLU GLN ILE ALA GLU PHE LEU GLU GLN SER SEQRES 36 A 645 VAL LYS ASP SER CYS GLU GLY LEU MET VAL LYS THR LEU SEQRES 37 A 645 ASP VAL ASP ALA THR TYR GLU ILE ALA LYS ARG SER HIS SEQRES 38 A 645 ASN TRP LEU LYS LEU LYS LYS ASP TYR LEU ASP GLY VAL SEQRES 39 A 645 GLY ASP THR LEU ASP LEU VAL VAL ILE GLY ALA TYR LEU SEQRES 40 A 645 GLY ARG GLY LYS ARG ALA GLY ARG TYR GLY GLY PHE LEU SEQRES 41 A 645 LEU ALA SER TYR ASP GLU ASP SER GLU GLU LEU GLN ALA SEQRES 42 A 645 ILE CYS LYS LEU GLY THR GLY PHE SER ASP GLU GLU LEU SEQRES 43 A 645 GLU GLU HIS HIS GLN SER LEU LYS ALA LEU VAL LEU PRO SEQRES 44 A 645 SER PRO ARG PRO TYR VAL ARG ILE ASP GLY ALA VAL ILE SEQRES 45 A 645 PRO ASP HIS TRP LEU ASP PRO SER ALA VAL TRP GLU VAL SEQRES 46 A 645 LYS CYS ALA ASP LEU SER LEU SER PRO ILE TYR PRO ALA SEQRES 47 A 645 ALA ARG GLY LEU VAL ASP SER ASP LYS GLY ILE SER LEU SEQRES 48 A 645 ARG PHE PRO ARG PHE ILE ARG VAL ARG GLU ASP LYS GLN SEQRES 49 A 645 PRO GLU GLN ALA THR THR SER ALA GLN VAL ALA CYS LEU SEQRES 50 A 645 TYR ARG LYS GLN SER GLN ILE GLN SEQRES 1 B 11 DG DC DT DG DA DT DG DC DG DT DC SEQRES 1 C 7 DG DT DC DG DG DA DC SEQRES 1 D 18 DG DT DC DC DG DA DC DG DA DC DG DC DA SEQRES 2 D 18 DT DC DA DG DC HET PEG A1001 17 HET AMP C 101 34 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 5 PEG C4 H10 O3 FORMUL 6 AMP C10 H14 N5 O7 P FORMUL 7 HOH *970(H2 O) HELIX 1 AA1 ASP A 262 TYR A 266 5 5 HELIX 2 AA2 PRO A 288 GLU A 301 1 14 HELIX 3 AA3 ALA A 304 SER A 323 1 20 HELIX 4 AA4 ASP A 326 ASN A 336 1 11 HELIX 5 AA5 PRO A 340 GLY A 344 5 5 HELIX 6 AA6 GLY A 350 GLY A 363 1 14 HELIX 7 AA7 GLN A 365 GLY A 377 1 13 HELIX 8 AA8 ASP A 378 ASN A 385 1 8 HELIX 9 AA9 THR A 400 LEU A 414 1 15 HELIX 10 AB1 ALA A 418 CYS A 434 1 17 HELIX 11 AB2 SER A 437 SER A 447 1 11 HELIX 12 AB3 ALA A 455 THR A 470 1 16 HELIX 13 AB4 THR A 488 VAL A 510 1 23 HELIX 14 AB5 ASP A 512 GLY A 524 1 13 HELIX 15 AB6 ARG A 527 CYS A 532 1 6 HELIX 16 AB7 GLY A 550 GLU A 559 1 10 HELIX 17 AB8 ASN A 594 LYS A 597 5 4 HELIX 18 AB9 TYR A 598 LYS A 609 1 12 HELIX 19 AC1 PRO A 634 THR A 639 1 6 HELIX 20 AC2 ASP A 647 ILE A 651 5 5 HELIX 21 AC3 PRO A 674 PHE A 686 1 13 HELIX 22 AC4 ASP A 703 ASP A 717 1 15 HELIX 23 AC5 ASP A 748 LEU A 750 5 3 HELIX 24 AC6 ARG A 768 ALA A 772 5 5 HELIX 25 AC7 SER A 801 ALA A 814 1 14 HELIX 26 AC8 GLN A 883 ALA A 887 5 5 HELIX 27 AC9 THR A 889 LYS A 899 1 11 SHEET 1 AA1 5 ALA A 545 PRO A 547 0 SHEET 2 AA1 5 TRP A 742 LYS A 746 1 O TRP A 742 N HIS A 546 SHEET 3 AA1 5 GLY A 721 THR A 726 -1 N LEU A 722 O LEU A 745 SHEET 4 AA1 5 PHE A 563 TYR A 567 -1 N GLU A 566 O MET A 723 SHEET 5 AA1 5 SER A 698 ASP A 700 -1 O LEU A 699 N CYS A 565 SHEET 1 AA2 5 VAL A 584 PHE A 587 0 SHEET 2 AA2 5 GLN A 572 ALA A 578 -1 N HIS A 577 O LYS A 585 SHEET 3 AA2 5 PHE A 616 ASP A 626 -1 O ALA A 622 N GLN A 572 SHEET 4 AA2 5 VAL A 655 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 5 AA2 5 GLU A 668 SER A 669 -1 O GLU A 668 N LEU A 665 SHEET 1 AA3 4 GLN A 631 ILE A 632 0 SHEET 2 AA3 4 PHE A 616 ASP A 626 -1 N ASP A 626 O GLN A 631 SHEET 3 AA3 4 VAL A 655 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 4 AA3 4 PHE A 693 PHE A 695 1 O VAL A 694 N LEU A 657 SHEET 1 AA4 6 VAL A 816 LEU A 817 0 SHEET 2 AA4 6 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA4 6 THR A 756 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA4 6 TYR A 775 ASP A 784 -1 O ALA A 781 N VAL A 760 SHEET 5 AA4 6 GLU A 789 LEU A 796 -1 O GLU A 789 N ASP A 784 SHEET 6 AA4 6 VAL A 824 ARG A 825 1 O ARG A 825 N LEU A 790 SHEET 1 AA5 5 VAL A 816 LEU A 817 0 SHEET 2 AA5 5 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA5 5 THR A 756 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA5 5 VAL A 841 LYS A 845 -1 O VAL A 844 N LEU A 757 SHEET 5 AA5 5 ARG A 874 VAL A 878 -1 O ARG A 877 N GLU A 843 SHEET 1 AA6 2 ASP A 848 SER A 852 0 SHEET 2 AA6 2 GLY A 867 ARG A 871 -1 O ARG A 871 N ASP A 848 LINK OP3 DG C 1 P AMP C 101 1555 1555 1.56 CISPEP 1 PHE A 476 PRO A 477 0 -2.56 SITE 1 AC1 3 ALA A 483 LYS A 487 TRP A 495 SITE 1 AC2 16 GLU A 566 TYR A 567 LYS A 568 TYR A 569 SITE 2 AC2 16 ARG A 573 GLU A 621 PHE A 660 MET A 723 SITE 3 AC2 16 LYS A 725 TRP A 742 LYS A 744 LYS A 746 SITE 4 AC2 16 HOH A1172 DG C 1 HOH C 201 HOH C 204 CRYST1 71.793 101.227 115.368 90.00 90.00 90.00 P 21 21 21 4 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 0.013929 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008668 0.00000