HEADER LIGASE 15-NOV-12 3W1G TITLE CRYSTAL STRUCTURE OF HUMAN DNA LIGASE IV-ARTEMIS COMPLEX (NATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC REGION, UNP RESIDUES 1-609; COMPND 5 SYNONYM: DNA LIGASE IV, POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] 4; COMPND 6 EC: 6.5.1.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ARTEMIS-DERIVED PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: DNA CROSS-LINK REPAIR 1C PROTEIN, PROTEIN A-SCID, SNM1 COMPND 12 HOMOLOG C, HSNM1C, SNM1-LIKE PROTEIN; COMPND 13 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: LIG4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINS; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS DNA LIGASE, NON HOMOLOGOUS END JOINING, DNA REPAIR, XRCC4, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.OCHI,T.L.BLUNDELL REVDAT 3 08-NOV-23 3W1G 1 REMARK SEQADV REVDAT 2 14-AUG-13 3W1G 1 JRNL REVDAT 1 03-APR-13 3W1G 0 JRNL AUTH T.OCHI,X.GU,T.L.BLUNDELL JRNL TITL STRUCTURE OF THE CATALYTIC REGION OF DNA LIGASE IV IN JRNL TITL 2 COMPLEX WITH AN ARTEMIS FRAGMENT SHEDS LIGHT ON JRNL TITL 3 DOUBLE-STRAND BREAK REPAIR JRNL REF STRUCTURE V. 21 672 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23523427 JRNL DOI 10.1016/J.STR.2013.02.014 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 27757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1388 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 59.4779 - 5.4926 0.89 2625 138 0.1827 0.2083 REMARK 3 2 5.4926 - 4.3600 0.93 2602 137 0.1428 0.1674 REMARK 3 3 4.3600 - 3.8090 0.95 2631 139 0.1434 0.2079 REMARK 3 4 3.8090 - 3.4608 0.95 2659 140 0.1656 0.2307 REMARK 3 5 3.4608 - 3.2127 0.96 2635 138 0.1875 0.2569 REMARK 3 6 3.2127 - 3.0233 0.96 2648 140 0.2057 0.2699 REMARK 3 7 3.0233 - 2.8719 0.96 2641 139 0.2221 0.2926 REMARK 3 8 2.8719 - 2.7469 0.97 2658 140 0.2264 0.3021 REMARK 3 9 2.7469 - 2.6412 0.97 2623 138 0.2431 0.3187 REMARK 3 10 2.6412 - 2.5500 0.97 2647 139 0.2664 0.3396 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.46 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 : 0.008 4823 REMARK 3 ANGLE : 1.153 6540 REMARK 3 CHIRALITY : 0.077 728 REMARK 3 PLANARITY : 0.004 812 REMARK 3 DIHEDRAL : 16.322 1748 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESSEQ 6:241 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4454 28.0532 174.7169 REMARK 3 T TENSOR REMARK 3 T11: 0.3214 T22: 0.3005 REMARK 3 T33: 0.2288 T12: -0.0048 REMARK 3 T13: -0.0412 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 3.1863 L22: 4.0276 REMARK 3 L33: 2.3659 L12: -1.6427 REMARK 3 L13: -0.1157 L23: 0.5014 REMARK 3 S TENSOR REMARK 3 S11: 0.0852 S12: 0.1404 S13: -0.0141 REMARK 3 S21: -0.0701 S22: 0.0739 S23: -0.0007 REMARK 3 S31: -0.0582 S32: 0.0534 S33: -0.1436 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESSEQ 242:454 REMARK 3 ORIGIN FOR THE GROUP (A): 18.7665 12.4266 143.8409 REMARK 3 T TENSOR REMARK 3 T11: 0.4225 T22: 0.4388 REMARK 3 T33: 0.4059 T12: 0.1007 REMARK 3 T13: -0.0361 T23: -0.1323 REMARK 3 L TENSOR REMARK 3 L11: 1.7257 L22: 1.3352 REMARK 3 L33: 4.4599 L12: 0.2139 REMARK 3 L13: 0.9215 L23: -0.9099 REMARK 3 S TENSOR REMARK 3 S11: 0.1232 S12: 0.0939 S13: -0.1485 REMARK 3 S21: -0.1282 S22: 0.0395 S23: -0.3404 REMARK 3 S31: 0.5254 S32: 0.6486 S33: -0.1504 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESSEQ 455:604 REMARK 3 ORIGIN FOR THE GROUP (A): 21.0982 34.8282 119.3496 REMARK 3 T TENSOR REMARK 3 T11: 0.3557 T22: 0.3623 REMARK 3 T33: 0.7260 T12: 0.0235 REMARK 3 T13: 0.1408 T23: -0.0700 REMARK 3 L TENSOR REMARK 3 L11: 5.1404 L22: 1.6803 REMARK 3 L33: 5.0291 L12: 1.3104 REMARK 3 L13: -0.3733 L23: -1.1817 REMARK 3 S TENSOR REMARK 3 S11: 0.1582 S12: 0.0364 S13: 0.8039 REMARK 3 S21: -0.0026 S22: -0.0458 S23: -0.2325 REMARK 3 S31: -0.3011 S32: 0.3126 S33: -0.1349 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 12.0360 22.1796 193.0496 REMARK 3 T TENSOR REMARK 3 T11: 0.7277 T22: 0.8252 REMARK 3 T33: 0.4139 T12: -0.0155 REMARK 3 T13: -0.1642 T23: 0.0338 REMARK 3 L TENSOR REMARK 3 L11: 7.8362 L22: 5.9824 REMARK 3 L33: 3.8478 L12: -6.3855 REMARK 3 L13: 3.8873 L23: -4.3894 REMARK 3 S TENSOR REMARK 3 S11: -0.9209 S12: -0.0412 S13: 0.6957 REMARK 3 S21: 0.8613 S22: 0.0230 S23: -0.1314 REMARK 3 S31: -1.1414 S32: 0.8416 S33: 0.8445 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND RESSEQ 701:701 REMARK 3 ORIGIN FOR THE GROUP (A): 21.3222 22.1853 144.3770 REMARK 3 T TENSOR REMARK 3 T11: 0.7553 T22: 0.9445 REMARK 3 T33: 1.4496 T12: -0.0721 REMARK 3 T13: -0.0377 T23: -0.0338 REMARK 3 L TENSOR REMARK 3 L11: 8.4913 L22: 7.8786 REMARK 3 L33: 5.6612 L12: -7.8822 REMARK 3 L13: 6.8733 L23: -6.6146 REMARK 3 S TENSOR REMARK 3 S11: -0.5686 S12: 0.6443 S13: -0.9188 REMARK 3 S21: 0.4949 S22: -0.0522 S23: 0.6934 REMARK 3 S31: -0.6747 S32: -0.6051 S33: 0.6139 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND RESSEQ 702:716 REMARK 3 ORIGIN FOR THE GROUP (A): 12.1148 21.5481 144.9984 REMARK 3 T TENSOR REMARK 3 T11: 1.2174 T22: 0.9231 REMARK 3 T33: 1.3637 T12: 0.0524 REMARK 3 T13: -0.0507 T23: -0.1550 REMARK 3 L TENSOR REMARK 3 L11: 0.5636 L22: 0.0959 REMARK 3 L33: 1.8606 L12: -0.1332 REMARK 3 L13: 0.9403 L23: -0.3935 REMARK 3 S TENSOR REMARK 3 S11: -0.0400 S12: 0.0767 S13: -0.0916 REMARK 3 S21: 0.0565 S22: -0.1351 S23: -0.2138 REMARK 3 S31: 0.6376 S32: 0.3588 S33: 0.2044 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN A AND RESSEQ 801:871 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2025 24.9769 156.2592 REMARK 3 T TENSOR REMARK 3 T11: 0.4690 T22: 0.4072 REMARK 3 T33: 0.3891 T12: 0.0202 REMARK 3 T13: 0.0295 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: -0.0403 L22: 0.0744 REMARK 3 L33: 0.0723 L12: -0.0083 REMARK 3 L13: -0.0043 L23: -0.1118 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: -0.0139 S13: -0.0205 REMARK 3 S21: -0.0363 S22: 0.1287 S23: -0.0118 REMARK 3 S31: -0.0248 S32: -0.1095 S33: -0.0000 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 3W1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000095765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27784 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 68.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: PDB ENTRY 3W1B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 10MM YCL, 100MM REMARK 280 MES, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.54000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.74000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.54000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -208.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 THR A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 GLN A 5 REMARK 465 PRO A 115 REMARK 465 THR A 116 REMARK 465 GLY A 117 REMARK 465 THR A 118 REMARK 465 HIS A 119 REMARK 465 GLY A 120 REMARK 465 ASP A 121 REMARK 465 ALA A 122 REMARK 465 GLY A 457 REMARK 465 LEU A 458 REMARK 465 ARG A 476 REMARK 465 GLY A 477 REMARK 465 PRO A 493 REMARK 465 GLY A 494 REMARK 465 GLU A 495 REMARK 465 LYS A 496 REMARK 465 LYS A 605 REMARK 465 ALA A 606 REMARK 465 SER A 607 REMARK 465 GLY A 608 REMARK 465 LYS A 609 REMARK 465 ASP B 485 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 GLN A 8 CG CD OE1 NE2 REMARK 470 LYS A 30 CG CD CE NZ REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ASN A 56 CG OD1 ND2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 ASP A 237 CG OD1 OD2 REMARK 470 ASP A 255 CG OD1 OD2 REMARK 470 GLU A 257 CG CD OE1 OE2 REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 LYS A 264 CG CD CE NZ REMARK 470 ASP A 275 CG OD1 OD2 REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 ASP A 322 CG OD1 OD2 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 LYS A 348 CG CD CE NZ REMARK 470 LYS A 352 CG CD CE NZ REMARK 470 ARG A 353 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 374 CG OD1 ND2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LYS A 384 CG CD CE NZ REMARK 470 ASN A 412 CG OD1 ND2 REMARK 470 VAL A 414 CG1 CG2 REMARK 470 GLU A 420 CG CD OE1 OE2 REMARK 470 GLU A 445 CG CD OE1 OE2 REMARK 470 GLU A 453 CG CD OE1 OE2 REMARK 470 GLU A 461 CG CD OE1 OE2 REMARK 470 SER A 475 OG REMARK 470 LYS A 490 CG CD CE NZ REMARK 470 ARG A 531 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 532 CG CD CE NZ REMARK 470 LYS A 588 CG CD CE NZ REMARK 470 ASP A 597 CG OD1 OD2 REMARK 470 GLN B 488 CG CD OE1 NE2 REMARK 470 GLU B 490 CG CD OE1 OE2 REMARK 470 ARG B 495 CG CD NE CZ NH1 NH2 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 NZ LYS A 273 O2G ATP A 701 2.16 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 ASP A 59 77.95 51.70 REMARK 500 ARG A 113 -79.69 -118.00 REMARK 500 HIS A 265 28.36 47.63 REMARK 500 LEU A 311 -58.34 -131.51 REMARK 500 ASN A 373 -119.55 50.28 REMARK 500 ASN A 374 33.16 -98.17 REMARK 500 ARG A 399 -56.54 -129.25 REMARK 500 HIS A 409 15.96 -141.63 REMARK 500 ARG A 425 17.86 59.58 REMARK 500 ASP A 441 -1.51 67.77 REMARK 500 GLU A 445 -114.67 56.03 REMARK 500 LYS A 473 153.19 -49.37 REMARK 500 LEU A 503 -42.84 -131.18 REMARK 500 PHE B 493 -71.05 -83.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 712 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 713 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 714 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 715 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 716 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF ARTEMIS-DERIVED REMARK 800 PEPTIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W1B RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MERCURY REMARK 900 RELATED ID: 3VNN RELATED DB: PDB REMARK 900 A SUB DOMAIN OF THE NTASE DOMAIN OF THE SAME PROTEIN REMARK 900 RELATED ID: 1IK9 RELATED DB: PDB REMARK 900 A DIFFERENT POLYPEPTIDE FROM THE SAME PROTEIN REMARK 900 RELATED ID: 3II6 RELATED DB: PDB REMARK 900 THE BRCT DOMAINS OF THE SAME PROTEIN REMARK 900 RELATED ID: 2E2W RELATED DB: PDB REMARK 900 THE FIRST BRCT DOMAIN OF THE SAME PROTEIN REMARK 900 RELATED ID: 1X9N RELATED DB: PDB REMARK 900 A HUMAN HOMOLOG REMARK 900 RELATED ID: 3W5O RELATED DB: PDB DBREF 3W1G A 1 609 UNP P49917 DNLI4_HUMAN 1 609 DBREF 3W1G B 485 495 UNP Q96SD1 DCR1C_HUMAN 485 495 SEQADV 3W1G THR A 0 UNP P49917 EXPRESSION TAG SEQRES 1 A 610 THR MET ALA ALA SER GLN THR SER GLN THR VAL ALA SER SEQRES 2 A 610 HIS VAL PRO PHE ALA ASP LEU CYS SER THR LEU GLU ARG SEQRES 3 A 610 ILE GLN LYS SER LYS GLY ARG ALA GLU LYS ILE ARG HIS SEQRES 4 A 610 PHE ARG GLU PHE LEU ASP SER TRP ARG LYS PHE HIS ASP SEQRES 5 A 610 ALA LEU HIS LYS ASN HIS LYS ASP VAL THR ASP SER PHE SEQRES 6 A 610 TYR PRO ALA MET ARG LEU ILE LEU PRO GLN LEU GLU ARG SEQRES 7 A 610 GLU ARG MET ALA TYR GLY ILE LYS GLU THR MET LEU ALA SEQRES 8 A 610 LYS LEU TYR ILE GLU LEU LEU ASN LEU PRO ARG ASP GLY SEQRES 9 A 610 LYS ASP ALA LEU LYS LEU LEU ASN TYR ARG THR PRO THR SEQRES 10 A 610 GLY THR HIS GLY ASP ALA GLY ASP PHE ALA MET ILE ALA SEQRES 11 A 610 TYR PHE VAL LEU LYS PRO ARG CYS LEU GLN LYS GLY SER SEQRES 12 A 610 LEU THR ILE GLN GLN VAL ASN ASP LEU LEU ASP SER ILE SEQRES 13 A 610 ALA SER ASN ASN SER ALA LYS ARG LYS ASP LEU ILE LYS SEQRES 14 A 610 LYS SER LEU LEU GLN LEU ILE THR GLN SER SER ALA LEU SEQRES 15 A 610 GLU GLN LYS TRP LEU ILE ARG MET ILE ILE LYS ASP LEU SEQRES 16 A 610 LYS LEU GLY VAL SER GLN GLN THR ILE PHE SER VAL PHE SEQRES 17 A 610 HIS ASN ASP ALA ALA GLU LEU HIS ASN VAL THR THR ASP SEQRES 18 A 610 LEU GLU LYS VAL CYS ARG GLN LEU HIS ASP PRO SER VAL SEQRES 19 A 610 GLY LEU SER ASP ILE SER ILE THR LEU PHE SER ALA PHE SEQRES 20 A 610 LYS PRO MET LEU ALA ALA ILE ALA ASP ILE GLU HIS ILE SEQRES 21 A 610 GLU LYS ASP MET LYS HIS GLN SER PHE TYR ILE GLU THR SEQRES 22 A 610 LYS LEU ASP GLY GLU ARG MET GLN MET HIS LYS ASP GLY SEQRES 23 A 610 ASP VAL TYR LYS TYR PHE SER ARG ASN GLY TYR ASN TYR SEQRES 24 A 610 THR ASP GLN PHE GLY ALA SER PRO THR GLU GLY SER LEU SEQRES 25 A 610 THR PRO PHE ILE HIS ASN ALA PHE LYS ALA ASP ILE GLN SEQRES 26 A 610 ILE CYS ILE LEU ASP GLY GLU MET MET ALA TYR ASN PRO SEQRES 27 A 610 ASN THR GLN THR PHE MET GLN LYS GLY THR LYS PHE ASP SEQRES 28 A 610 ILE LYS ARG MET VAL GLU ASP SER ASP LEU GLN THR CYS SEQRES 29 A 610 TYR CYS VAL PHE ASP VAL LEU MET VAL ASN ASN LYS LYS SEQRES 30 A 610 LEU GLY HIS GLU THR LEU ARG LYS ARG TYR GLU ILE LEU SEQRES 31 A 610 SER SER ILE PHE THR PRO ILE PRO GLY ARG ILE GLU ILE SEQRES 32 A 610 VAL GLN LYS THR GLN ALA HIS THR LYS ASN GLU VAL ILE SEQRES 33 A 610 ASP ALA LEU ASN GLU ALA ILE ASP LYS ARG GLU GLU GLY SEQRES 34 A 610 ILE MET VAL LYS GLN PRO LEU SER ILE TYR LYS PRO ASP SEQRES 35 A 610 LYS ARG GLY GLU GLY TRP LEU LYS ILE LYS PRO GLU TYR SEQRES 36 A 610 VAL SER GLY LEU MET ASP GLU LEU ASP ILE LEU ILE VAL SEQRES 37 A 610 GLY GLY TYR TRP GLY LYS GLY SER ARG GLY GLY MET MET SEQRES 38 A 610 SER HIS PHE LEU CYS ALA VAL ALA GLU LYS PRO PRO PRO SEQRES 39 A 610 GLY GLU LYS PRO SER VAL PHE HIS THR LEU SER ARG VAL SEQRES 40 A 610 GLY SER GLY CYS THR MET LYS GLU LEU TYR ASP LEU GLY SEQRES 41 A 610 LEU LYS LEU ALA LYS TYR TRP LYS PRO PHE HIS ARG LYS SEQRES 42 A 610 ALA PRO PRO SER SER ILE LEU CYS GLY THR GLU LYS PRO SEQRES 43 A 610 GLU VAL TYR ILE GLU PRO CYS ASN SER VAL ILE VAL GLN SEQRES 44 A 610 ILE LYS ALA ALA GLU ILE VAL PRO SER ASP MET TYR LYS SEQRES 45 A 610 THR GLY CYS THR LEU ARG PHE PRO ARG ILE GLU LYS ILE SEQRES 46 A 610 ARG ASP ASP LYS GLU TRP HIS GLU CYS MET THR LEU ASP SEQRES 47 A 610 ASP LEU GLU GLN LEU ARG GLY LYS ALA SER GLY LYS SEQRES 1 B 11 ASP VAL PRO GLN TRP GLU VAL PHE PHE LYS ARG HET ATP A 701 31 HET SO4 A 702 5 HET SO4 A 703 5 HET SO4 A 704 5 HET SO4 A 705 5 HET SO4 A 706 5 HET SO4 A 707 5 HET SO4 A 708 5 HET SO4 A 709 5 HET SO4 A 710 5 HET SO4 A 711 5 HET SO4 A 712 5 HET SO4 A 713 5 HET SO4 A 714 5 HET SO4 A 715 5 HET SO4 A 716 5 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 SO4 15(O4 S 2-) FORMUL 19 HOH *71(H2 O) HELIX 1 1 THR A 9 HIS A 13 5 5 HELIX 2 2 PRO A 15 SER A 29 1 15 HELIX 3 3 GLY A 31 LYS A 55 1 25 HELIX 4 4 PHE A 64 LEU A 72 1 9 HELIX 5 5 PRO A 73 GLU A 76 5 4 HELIX 6 6 LYS A 85 ASN A 98 1 14 HELIX 7 7 GLY A 103 ASN A 111 1 9 HELIX 8 8 ASP A 124 CYS A 137 1 14 HELIX 9 9 THR A 144 ALA A 161 1 18 HELIX 10 10 ARG A 163 GLN A 177 1 15 HELIX 11 11 SER A 179 LYS A 192 1 14 HELIX 12 12 SER A 199 HIS A 208 1 10 HELIX 13 13 ASP A 210 THR A 218 1 9 HELIX 14 14 ASP A 220 LEU A 228 1 9 HELIX 15 15 ASP A 255 GLU A 257 5 3 HELIX 16 16 HIS A 258 MET A 263 1 6 HELIX 17 17 TYR A 298 GLY A 303 1 6 HELIX 18 18 LEU A 311 HIS A 316 1 6 HELIX 19 19 ASN A 317 PHE A 319 5 3 HELIX 20 20 ASP A 350 ASP A 357 1 8 HELIX 21 21 THR A 381 PHE A 393 1 13 HELIX 22 22 THR A 410 LYS A 424 1 15 HELIX 23 23 MET A 512 ALA A 523 1 12 HELIX 24 24 GLU A 550 SER A 554 5 5 HELIX 25 25 GLU A 589 CYS A 593 5 5 HELIX 26 26 THR A 595 GLY A 604 1 10 HELIX 27 27 TRP B 489 LYS B 494 1 6 SHEET 1 A 5 LEU A 250 ILE A 253 0 SHEET 2 A 5 ARG A 443 ILE A 450 1 O LYS A 449 N ALA A 252 SHEET 3 A 5 ILE A 429 LYS A 432 -1 N VAL A 431 O LEU A 448 SHEET 4 A 5 PHE A 268 THR A 272 -1 N GLU A 271 O MET A 430 SHEET 5 A 5 LYS A 405 ALA A 408 -1 O THR A 406 N ILE A 270 SHEET 1 B 5 VAL A 287 SER A 292 0 SHEET 2 B 5 GLU A 277 ASP A 284 -1 N HIS A 282 O LYS A 289 SHEET 3 B 5 ILE A 325 ASN A 336 -1 O MET A 332 N GLU A 277 SHEET 4 B 5 GLN A 361 VAL A 372 -1 O GLN A 361 N TYR A 335 SHEET 5 B 5 LYS A 375 LYS A 376 -1 O LYS A 375 N VAL A 372 SHEET 1 C 4 THR A 341 MET A 343 0 SHEET 2 C 4 ILE A 325 ASN A 336 -1 N ALA A 334 O MET A 343 SHEET 3 C 4 GLN A 361 VAL A 372 -1 O GLN A 361 N TYR A 335 SHEET 4 C 4 ILE A 400 ILE A 402 1 O GLU A 401 N VAL A 366 SHEET 1 D 6 LYS A 527 PRO A 528 0 SHEET 2 D 6 VAL A 547 TYR A 548 -1 O TYR A 548 N LYS A 527 SHEET 3 D 6 LEU A 462 TRP A 471 -1 N GLY A 469 O VAL A 547 SHEET 4 D 6 MET A 480 ALA A 488 -1 O LEU A 484 N GLY A 468 SHEET 5 D 6 PHE A 500 GLY A 507 -1 O SER A 504 N CYS A 485 SHEET 6 D 6 ILE A 538 LEU A 539 1 O LEU A 539 N PHE A 500 SHEET 1 E 5 LYS A 527 PRO A 528 0 SHEET 2 E 5 VAL A 547 TYR A 548 -1 O TYR A 548 N LYS A 527 SHEET 3 E 5 LEU A 462 TRP A 471 -1 N GLY A 469 O VAL A 547 SHEET 4 E 5 ILE A 556 LYS A 560 -1 O ILE A 559 N LEU A 462 SHEET 5 E 5 ARG A 580 ARG A 585 -1 O GLU A 582 N GLN A 558 SHEET 1 F 2 GLU A 563 PRO A 566 0 SHEET 2 F 2 CYS A 574 ARG A 577 -1 O ARG A 577 N GLU A 563 SITE 1 AC1 15 GLU A 271 THR A 272 LYS A 273 LEU A 274 SITE 2 AC1 15 ASP A 275 GLU A 331 PHE A 367 GLU A 427 SITE 3 AC1 15 MET A 430 LYS A 432 TRP A 447 LYS A 449 SITE 4 AC1 15 LYS A 451 SO4 A 709 HOH A 871 SITE 1 AC2 4 GLY A 276 GLU A 277 ARG A 278 ARG A 293 SITE 1 AC3 4 SER A 292 ASN A 294 TYR A 296 TYR A 298 SITE 1 AC4 5 ASN A 297 TYR A 298 ASP A 300 GLN A 301 SITE 2 AC4 5 SO4 A 705 SITE 1 AC5 3 ASN A 297 SO4 A 704 HOH A 845 SITE 1 AC6 4 ARG A 32 VAL A 198 SER A 199 THR A 202 SITE 1 AC7 5 HIS A 50 VAL A 60 ASP A 62 ARG A 226 SITE 2 AC7 5 HIS A 229 SITE 1 AC8 2 ARG A 163 HIS A 530 SITE 1 AC9 5 ARG A 293 ARG A 443 LYS A 449 ATP A 701 SITE 2 AC9 5 HOH A 871 SITE 1 BC1 2 ARG A 163 LYS A 527 SITE 1 BC2 4 PHE A 529 HIS A 530 ARG A 531 LYS A 532 SITE 1 BC3 2 LYS A 544 HOH A 867 SITE 1 BC4 5 LEU A 214 GLN A 227 LEU A 235 SER A 239 SITE 2 BC4 5 THR A 241 SITE 1 BC5 3 LYS A 162 LYS A 164 ASP A 165 SITE 1 BC6 1 GLU A 277 SITE 1 BC7 8 THR A 341 LYS A 473 GLY A 474 SER A 475 SITE 2 BC7 8 MET A 479 MET A 480 GLY A 509 CYS A 510 SITE 1 BC8 9 HIS A 13 VAL A 14 PRO A 15 ASP A 18 SITE 2 BC8 9 ARG A 25 SER A 45 LYS A 48 PHE A 49 SITE 3 BC8 9 ALA A 52 CRYST1 68.260 105.480 121.080 90.00 90.00 90.00 P 2 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 0.014650 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008259 0.00000