HEADER LIGASE/DNA 01-OCT-25 9YHV TITLE DNA LIGASE 1 E346A/E592A IN COMPLEX WITH NICK CONTAINING 3'-8OXORG:C TITLE 2 CAPTURED AT PRE-CATALYTIC STAGE 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(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(8GM))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*(AMP)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(P*GP*TP*CP*CP*GP*AP*CP*CP*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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS DNA BINDING PROTEIN, DNA REPAIR, BER, HUMAN DNA LIGASE 1, LIGASE, KEYWDS 2 LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.KANALELAMPARITHI,M.CAGLAYAN REVDAT 1 31-DEC-25 9YHV 0 JRNL AUTH K.E.BALU,D.ALMOHDAR,C.LERNER,J.RATCLIFFE,Q.TANG,T.PARWAL, JRNL AUTH 2 K.M.LEE,A.PRAKASH,M.CAGLAYAN JRNL TITL PROCESSING OF DNA SINGLE-STRAND BREAKS WITH OXIDATIVELY JRNL TITL 2 DAMAGED ENDS BY LIG1. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 41370201 JRNL DOI 10.1093/NAR/GKAF1344 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.1_5286: ???) 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2004 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 36.8300 - 6.7500 0.99 1639 155 0.2030 0.2484 REMARK 3 2 6.7500 - 5.3700 1.00 1570 148 0.2393 0.2409 REMARK 3 3 5.3700 - 4.6900 1.00 1547 150 0.1937 0.2606 REMARK 3 4 4.6900 - 4.2600 1.00 1535 133 0.1840 0.2390 REMARK 3 5 4.2600 - 3.9600 1.00 1527 148 0.1914 0.1970 REMARK 3 6 3.9600 - 3.7200 1.00 1524 150 0.2279 0.2851 REMARK 3 7 3.7200 - 3.5400 1.00 1525 139 0.2441 0.2888 REMARK 3 8 3.5400 - 3.3800 0.99 1494 138 0.2278 0.3041 REMARK 3 9 3.3800 - 3.2500 0.96 1464 130 0.2473 0.2763 REMARK 3 10 3.2500 - 3.1400 0.98 1452 149 0.2609 0.2897 REMARK 3 11 3.1400 - 3.0400 1.00 1512 130 0.2708 0.3172 REMARK 3 12 3.0400 - 2.9600 1.00 1506 155 0.2965 0.3579 REMARK 3 13 2.9600 - 2.8800 1.00 1497 131 0.2959 0.3251 REMARK 3 14 2.8800 - 2.8100 1.00 1500 148 0.3252 0.3686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.002 5105 REMARK 3 ANGLE : 0.515 7115 REMARK 3 CHIRALITY : 0.036 827 REMARK 3 PLANARITY : 0.004 811 REMARK 3 DIHEDRAL : 20.258 1829 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -4.9883 12.5426 -31.8083 REMARK 3 T TENSOR REMARK 3 T11: 0.5823 T22: 0.2978 REMARK 3 T33: 0.5381 T12: 0.0483 REMARK 3 T13: 0.0240 T23: 0.0663 REMARK 3 L TENSOR REMARK 3 L11: 1.6455 L22: 2.8182 REMARK 3 L33: 2.5344 L12: 0.0446 REMARK 3 L13: -0.0003 L23: 0.0073 REMARK 3 S TENSOR REMARK 3 S11: -0.1693 S12: -0.1250 S13: -0.0504 REMARK 3 S21: 0.0411 S22: 0.2668 S23: 0.0999 REMARK 3 S31: -0.0149 S32: -0.1322 S33: -0.1085 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 9YHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000300591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-23 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23296 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 36.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.88 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES (PH 6.0), 150 MM LITHIUM REMARK 280 ACETATE, 16% (W/V) PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K 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 32.06100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.83950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.78950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.83950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.06100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.78950 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: 6940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 388 REMARK 465 THR A 389 REMARK 465 GLN A 390 REMARK 465 ARG A 391 REMARK 465 LEU A 392 REMARK 465 MET A 393 REMARK 465 VAL A 554 REMARK 465 LEU A 555 REMARK 465 LYS A 556 REMARK 465 ARG A 557 REMARK 465 PHE A 558 REMARK 465 GLU A 559 REMARK 465 GLU A 560 REMARK 465 ALA A 561 REMARK 465 ALA A 562 REMARK 465 THR A 697 REMARK 465 SER A 698 REMARK 465 LEU A 699 REMARK 465 ASP A 700 REMARK 465 GLU A 720 REMARK 465 GLY A 721 REMARK 465 LYS A 747 REMARK 465 ASP A 748 REMARK 465 TYR A 749 REMARK 465 LEU A 750 REMARK 465 ASP A 751 REMARK 465 GLY A 752 REMARK 465 VAL A 753 REMARK 465 GLY A 754 REMARK 465 ASP A 755 REMARK 465 GLN A 902 REMARK 465 ILE A 903 REMARK 465 GLN A 904 REMARK 465 ASN A 905 REMARK 465 GLN A 906 REMARK 465 GLN A 907 REMARK 465 GLY A 908 REMARK 465 GLU A 909 REMARK 465 ASP A 910 REMARK 465 SER A 911 REMARK 465 GLY A 912 REMARK 465 SER A 913 REMARK 465 ASP A 914 REMARK 465 PRO A 915 REMARK 465 GLU A 916 REMARK 465 ASP A 917 REMARK 465 THR A 918 REMARK 465 ALA A 919 REMARK 465 ALA A 920 REMARK 465 ALA A 921 REMARK 465 LEU A 922 REMARK 465 GLU A 923 REMARK 465 HIS A 924 REMARK 465 HIS A 925 REMARK 465 HIS A 926 REMARK 465 HIS A 927 REMARK 465 HIS A 928 REMARK 465 HIS A 929 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 ASP A 262 CG OD1 OD2 REMARK 470 SER A 264 OG REMARK 470 LYS A 270 CE NZ REMARK 470 ASN A 272 CG OD1 ND2 REMARK 470 GLU A 277 CG CD OE1 OE2 REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 GLN A 285 CG CD OE1 NE2 REMARK 470 LYS A 286 CD CE NZ REMARK 470 GLU A 301 CG CD OE1 OE2 REMARK 470 LEU A 306 CD1 CD2 REMARK 470 VAL A 320 CG1 CG2 REMARK 470 LEU A 322 CD1 REMARK 470 GLN A 343 CB CG CD OE1 NE2 REMARK 470 ASP A 351 CB CG OD1 OD2 REMARK 470 LYS A 356 CD CE NZ REMARK 470 ALA A 357 CB REMARK 470 VAL A 358 CG1 CG2 REMARK 470 ALA A 359 CB REMARK 470 ALA A 361 CB REMARK 470 THR A 362 CB OG1 CG2 REMARK 470 ARG A 364 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN A 365 CG CD OE1 NE2 REMARK 470 LEU A 366 CD1 CD2 REMARK 470 GLU A 367 CG CD OE1 OE2 REMARK 470 SER A 368 OG REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 GLU A 375 CG CD OE1 OE2 REMARK 470 LYS A 376 CD CE NZ REMARK 470 VAL A 379 CG1 CG2 REMARK 470 LEU A 381 CG CD1 CD2 REMARK 470 ASN A 385 CB CG OD1 ND2 REMARK 470 SER A 386 OG REMARK 470 ARG A 387 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 394 N CA CB CG CD1 CD2 REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 ASP A 425 CG OD1 OD2 REMARK 470 LYS A 428 CG CD CE NZ REMARK 470 ARG A 435 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 440 CZ NH1 NH2 REMARK 470 ARG A 449 CZ NH1 NH2 REMARK 470 ARG A 451 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 475 CG CD OE1 OE2 REMARK 470 PHE A 476 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PRO A 477 CG CD REMARK 470 PRO A 478 CG CD REMARK 470 VAL A 481 CG1 CG2 REMARK 470 LYS A 485 CG CD CE NZ REMARK 470 GLU A 490 CG CD OE1 OE2 REMARK 470 LYS A 493 CE NZ REMARK 470 ILE A 502 CD1 REMARK 470 GLU A 522 CD OE1 OE2 REMARK 470 GLU A 526 CG CD OE1 OE2 REMARK 470 ARG A 527 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 529 CG CD REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 HIS A 531 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 LEU A 534 CD1 CD2 REMARK 470 SER A 535 OG REMARK 470 LEU A 540 CD1 CD2 REMARK 470 HIS A 546 CG ND1 CD2 CE1 NE2 REMARK 470 PRO A 547 CG CD REMARK 470 THR A 548 OG1 CG2 REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 551 CG1 CG2 CD1 REMARK 470 GLU A 553 CG CD OE1 OE2 REMARK 470 PHE A 563 CG CD1 CD2 CE1 CE2 CZ REMARK 470 CYS A 565 SG REMARK 470 LYS A 568 CG CD CE NZ REMARK 470 TYR A 569 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 576 CD1 REMARK 470 GLU A 580 CG CD OE1 OE2 REMARK 470 VAL A 584 CG1 CG2 REMARK 470 LYS A 585 CE NZ REMARK 470 SER A 603 OG REMARK 470 ARG A 604 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 605 CG1 CG2 CD1 REMARK 470 LYS A 607 CB CG CD CE NZ REMARK 470 ILE A 608 CG1 CG2 CD1 REMARK 470 LYS A 609 CG CD CE NZ REMARK 470 PRO A 611 CG CD REMARK 470 SER A 612 OG REMARK 470 VAL A 613 CG1 CG2 REMARK 470 SER A 615 OG REMARK 470 GLU A 621 OE1 OE2 REMARK 470 ASP A 626 CG OD1 OD2 REMARK 470 GLU A 628 CG CD OE1 OE2 REMARK 470 LYS A 629 CG CD CE NZ REMARK 470 LYS A 630 CG CD CE NZ REMARK 470 GLN A 631 CG CD OE1 NE2 REMARK 470 ILE A 632 CG1 CG2 CD1 REMARK 470 GLN A 636 CG CD OE1 NE2 REMARK 470 VAL A 637 CG1 CG2 REMARK 470 LYS A 642 CG CD CE NZ REMARK 470 ARG A 643 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 644 CG CD CE NZ REMARK 470 GLU A 645 CG CD OE1 OE2 REMARK 470 VAL A 646 CG1 CG2 REMARK 470 ASP A 647 CG OD1 OD2 REMARK 470 SER A 649 OG REMARK 470 GLU A 650 CG CD OE1 OE2 REMARK 470 GLN A 652 CG CD OE1 NE2 REMARK 470 GLN A 654 OE1 NE2 REMARK 470 VAL A 655 CG1 CG2 REMARK 470 CYS A 656 SG REMARK 470 TYR A 658 CE1 CE2 CZ OH REMARK 470 ILE A 663 CG1 CG2 CD1 REMARK 470 LEU A 665 CG CD1 CD2 REMARK 470 GLU A 668 CG CD OE1 OE2 REMARK 470 VAL A 671 CG1 CG2 REMARK 470 ARG A 672 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 675 CG CD1 CD2 REMARK 470 SER A 676 OG REMARK 470 ARG A 677 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 679 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 680 CG CD OE1 NE2 REMARK 470 LEU A 681 CG CD1 CD2 REMARK 470 LEU A 682 CD1 CD2 REMARK 470 ARG A 683 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 684 CG CD OE1 OE2 REMARK 470 PHE A 686 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 687 CG1 CG2 REMARK 470 THR A 689 OG1 CG2 REMARK 470 GLU A 690 CG CD OE1 OE2 REMARK 470 PHE A 693 CE1 CZ REMARK 470 VAL A 694 CG1 CG2 REMARK 470 PHE A 695 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR A 701 OG1 CG2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 ILE A 704 CG1 CG2 CD1 REMARK 470 GLU A 705 CG CD OE1 OE2 REMARK 470 ILE A 707 CG1 CG2 CD1 REMARK 470 GLU A 709 CD OE1 OE2 REMARK 470 PHE A 710 CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 711 CG CD1 CD2 REMARK 470 GLU A 712 CG CD OE1 OE2 REMARK 470 GLN A 713 CD OE1 NE2 REMARK 470 SER A 714 OG REMARK 470 VAL A 715 CG1 CG2 REMARK 470 LYS A 716 CD CE NZ REMARK 470 SER A 718 CB OG REMARK 470 LEU A 722 CG CD1 CD2 REMARK 470 VAL A 724 CG1 CG2 REMARK 470 LYS A 725 CE NZ REMARK 470 THR A 726 OG1 CG2 REMARK 470 LEU A 727 CG CD1 CD2 REMARK 470 VAL A 729 CG1 CG2 REMARK 470 GLU A 734 CG CD OE1 OE2 REMARK 470 ILE A 735 CD1 REMARK 470 LYS A 737 CG CD CE NZ REMARK 470 ARG A 738 CG CD NE CZ NH1 NH2 REMARK 470 SER A 739 OG REMARK 470 HIS A 740 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 743 CG CD1 CD2 REMARK 470 LYS A 744 CG CD CE NZ REMARK 470 LEU A 745 CD1 CD2 REMARK 470 LYS A 746 CG CD CE NZ REMARK 470 LEU A 766 CD1 CD2 REMARK 470 ARG A 768 CZ NH1 NH2 REMARK 470 TYR A 783 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 786 CG OD1 OD2 REMARK 470 GLU A 788 CG CD OE1 OE2 REMARK 470 GLU A 803 CG CD OE1 OE2 REMARK 470 GLU A 804 CD OE1 OE2 REMARK 470 GLN A 810 CG CD OE1 NE2 REMARK 470 SER A 811 OG REMARK 470 LEU A 812 CD1 CD2 REMARK 470 LYS A 813 CG CD CE NZ REMARK 470 VAL A 816 CG1 CG2 REMARK 470 ILE A 831 CD1 REMARK 470 LEU A 836 CG CD1 CD2 REMARK 470 GLU A 843 CG CD OE1 OE2 REMARK 470 LYS A 845 CD CE NZ REMARK 470 ILE A 854 CD1 REMARK 470 VAL A 862 CG1 CG2 REMARK 470 SER A 864 OG REMARK 470 ILE A 868 CD1 REMARK 470 ARG A 877 NH1 NH2 REMARK 470 GLU A 880 CD OE1 OE2 REMARK 470 LYS A 882 CG CD CE NZ REMARK 470 GLU A 885 CG CD OE1 OE2 REMARK 470 LYS A 899 CG CD CE NZ REMARK 470 SER A 901 OG 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 12 OP1 - P - OP2 ANGL. DEV. = -9.9 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 362 138.14 -177.02 REMARK 500 ARG A 364 -142.35 62.85 REMARK 500 GLN A 365 74.18 52.06 REMARK 500 ALA A 418 15.15 58.43 REMARK 500 HIS A 436 -115.55 60.70 REMARK 500 ALA A 455 -150.72 -137.80 REMARK 500 ARG A 604 21.33 -149.34 REMARK 500 PHE A 660 -9.60 -143.39 REMARK 500 LEU A 665 106.08 -160.87 REMARK 500 GLU A 692 -74.32 -106.85 REMARK 500 ASP A 728 -47.65 -133.48 REMARK 500 ARG A 774 -165.75 -107.55 REMARK 500 ASP A 827 -102.51 61.37 REMARK 500 SER A 839 -23.49 -152.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YHV A 262 918 UNP P18858 DNLI1_HUMAN 262 918 DBREF 9YHV B 1 11 PDB 9YHV 9YHV 1 11 DBREF 9YHV C 11 18 PDB 9YHV 9YHV 11 18 DBREF 9YHV D 1 18 PDB 9YHV 9YHV 1 18 SEQADV 9YHV ALA A 346 UNP P18858 GLU 346 ENGINEERED MUTATION SEQADV 9YHV ALA A 592 UNP P18858 GLU 592 ENGINEERED MUTATION SEQADV 9YHV ALA A 919 UNP P18858 EXPRESSION TAG SEQADV 9YHV ALA A 920 UNP P18858 EXPRESSION TAG SEQADV 9YHV ALA A 921 UNP P18858 EXPRESSION TAG SEQADV 9YHV LEU A 922 UNP P18858 EXPRESSION TAG SEQADV 9YHV GLU A 923 UNP P18858 EXPRESSION TAG SEQADV 9YHV HIS A 924 UNP P18858 EXPRESSION TAG SEQADV 9YHV HIS A 925 UNP P18858 EXPRESSION TAG SEQADV 9YHV HIS A 926 UNP P18858 EXPRESSION TAG SEQADV 9YHV HIS A 927 UNP P18858 EXPRESSION TAG SEQADV 9YHV HIS A 928 UNP P18858 EXPRESSION TAG SEQADV 9YHV HIS A 929 UNP P18858 EXPRESSION TAG SEQRES 1 A 668 ASP PRO SER GLY TYR ASN PRO ALA LYS ASN ASN TYR HIS SEQRES 2 A 668 PRO VAL GLU ASP ALA CYS TRP LYS PRO GLY GLN LYS VAL SEQRES 3 A 668 PRO TYR LEU ALA VAL ALA ARG THR PHE GLU LYS ILE GLU SEQRES 4 A 668 GLU VAL SER ALA ARG LEU ARG MET VAL GLU THR LEU SER SEQRES 5 A 668 ASN LEU LEU ARG SER VAL VAL ALA LEU SER PRO PRO ASP SEQRES 6 A 668 LEU LEU PRO VAL LEU TYR LEU SER LEU ASN HIS LEU GLY SEQRES 7 A 668 PRO PRO GLN GLN GLY LEU ALA LEU GLY VAL GLY ASP GLY SEQRES 8 A 668 VAL LEU LEU LYS ALA VAL ALA GLN ALA THR GLY ARG GLN SEQRES 9 A 668 LEU GLU SER VAL ARG ALA GLU ALA ALA GLU LYS GLY ASP SEQRES 10 A 668 VAL GLY LEU VAL ALA GLU ASN SER ARG SER THR GLN ARG SEQRES 11 A 668 LEU MET LEU PRO PRO PRO PRO LEU THR ALA SER GLY VAL SEQRES 12 A 668 PHE SER LYS PHE ARG ASP ILE ALA ARG LEU THR GLY SER SEQRES 13 A 668 ALA SER THR ALA LYS LYS ILE ASP ILE ILE LYS GLY LEU SEQRES 14 A 668 PHE VAL ALA CYS ARG HIS SER GLU ALA ARG PHE ILE ALA SEQRES 15 A 668 ARG SER LEU SER GLY ARG LEU ARG LEU GLY LEU ALA GLU SEQRES 16 A 668 GLN SER VAL LEU ALA ALA LEU SER GLN ALA VAL SER LEU SEQRES 17 A 668 THR PRO PRO GLY GLN GLU PHE PRO PRO ALA MET VAL ASP SEQRES 18 A 668 ALA GLY LYS GLY LYS THR ALA GLU ALA ARG LYS THR TRP SEQRES 19 A 668 LEU GLU GLU GLN GLY MET ILE LEU LYS GLN THR PHE CYS SEQRES 20 A 668 GLU VAL PRO ASP LEU ASP ARG ILE ILE PRO VAL LEU LEU SEQRES 21 A 668 GLU HIS GLY LEU GLU ARG LEU PRO GLU HIS CYS LYS LEU SEQRES 22 A 668 SER PRO GLY ILE PRO LEU LYS PRO MET LEU ALA HIS PRO SEQRES 23 A 668 THR ARG GLY ILE SER GLU VAL LEU LYS ARG PHE GLU GLU SEQRES 24 A 668 ALA ALA PHE THR CYS GLU TYR LYS TYR ASP GLY GLN ARG SEQRES 25 A 668 ALA GLN ILE HIS ALA LEU GLU GLY GLY GLU VAL LYS ILE SEQRES 26 A 668 PHE SER ARG ASN GLN ALA ASP ASN THR GLY LYS TYR PRO SEQRES 27 A 668 ASP ILE ILE SER ARG ILE PRO LYS ILE LYS LEU PRO SER SEQRES 28 A 668 VAL THR SER PHE ILE LEU ASP THR GLU ALA VAL ALA TRP SEQRES 29 A 668 ASP ARG GLU LYS LYS GLN ILE GLN PRO PHE GLN VAL LEU SEQRES 30 A 668 THR THR ARG LYS ARG LYS GLU VAL ASP ALA SER GLU ILE SEQRES 31 A 668 GLN VAL GLN VAL CYS LEU TYR ALA PHE ASP LEU ILE TYR SEQRES 32 A 668 LEU ASN GLY GLU SER LEU VAL ARG GLU PRO LEU SER ARG SEQRES 33 A 668 ARG ARG GLN LEU LEU ARG GLU ASN PHE VAL GLU THR GLU SEQRES 34 A 668 GLY GLU PHE VAL PHE ALA THR SER LEU ASP THR LYS ASP SEQRES 35 A 668 ILE GLU GLN ILE ALA GLU PHE LEU GLU GLN SER VAL LYS SEQRES 36 A 668 ASP SER CYS GLU GLY LEU MET VAL LYS THR LEU ASP VAL SEQRES 37 A 668 ASP ALA THR TYR GLU ILE ALA LYS ARG SER HIS ASN TRP SEQRES 38 A 668 LEU LYS LEU LYS LYS ASP TYR LEU ASP GLY VAL GLY ASP SEQRES 39 A 668 THR LEU ASP LEU VAL VAL ILE GLY ALA TYR LEU GLY ARG SEQRES 40 A 668 GLY LYS ARG ALA GLY ARG TYR GLY GLY PHE LEU LEU ALA SEQRES 41 A 668 SER TYR ASP GLU ASP SER GLU GLU LEU GLN ALA ILE CYS SEQRES 42 A 668 LYS LEU GLY THR GLY PHE SER ASP GLU GLU LEU GLU GLU SEQRES 43 A 668 HIS HIS GLN SER LEU LYS ALA LEU VAL LEU PRO SER PRO SEQRES 44 A 668 ARG PRO TYR VAL ARG ILE ASP GLY ALA VAL ILE PRO ASP SEQRES 45 A 668 HIS TRP LEU ASP PRO SER ALA VAL TRP GLU VAL LYS CYS SEQRES 46 A 668 ALA ASP LEU SER LEU SER PRO ILE TYR PRO ALA ALA ARG SEQRES 47 A 668 GLY LEU VAL ASP SER ASP LYS GLY ILE SER LEU ARG PHE SEQRES 48 A 668 PRO ARG PHE ILE ARG VAL ARG GLU ASP LYS GLN PRO GLU SEQRES 49 A 668 GLN ALA THR THR SER ALA GLN VAL ALA CYS LEU TYR ARG SEQRES 50 A 668 LYS GLN SER GLN ILE GLN ASN GLN GLN GLY GLU ASP SER SEQRES 51 A 668 GLY SER ASP PRO GLU ASP THR ALA ALA ALA LEU GLU HIS SEQRES 52 A 668 HIS HIS HIS HIS HIS SEQRES 1 B 11 DG DC DT DG DA DT DG DC DG DT 8GM SEQRES 1 C 8 AMP DG DT DC DG DG DA DC SEQRES 1 D 18 DG DT DC DC DG DA DC DC DA DC DG DC DA SEQRES 2 D 18 DT DC DA DG DC HET 8GM B 11 24 HET AMP C 11 23 HETNAM 8GM [(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7- HETNAM 2 8GM DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 8GM DIHYDROGEN PHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN 8GM 8-OXOGUANOSINE-5'-PHOSPHATE FORMUL 2 8GM C10 H14 N5 O9 P FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 5 HOH *52(H2 O) HELIX 1 AA1 ASP A 262 TYR A 266 5 5 HELIX 2 AA2 PRO A 288 VAL A 302 1 15 HELIX 3 AA3 ALA A 304 LEU A 322 1 19 HELIX 4 AA4 SER A 323 PRO A 325 5 3 HELIX 5 AA5 ASP A 326 ASN A 336 1 11 HELIX 6 AA6 PRO A 340 GLY A 344 5 5 HELIX 7 AA7 GLY A 350 THR A 362 1 13 HELIX 8 AA8 GLN A 365 GLY A 377 1 13 HELIX 9 AA9 ASP A 378 SER A 386 1 9 HELIX 10 AB1 THR A 400 LEU A 414 1 15 HELIX 11 AB2 ALA A 418 ALA A 433 1 16 HELIX 12 AB3 SER A 437 SER A 447 1 11 HELIX 13 AB4 ALA A 455 THR A 470 1 16 HELIX 14 AB5 THR A 488 VAL A 510 1 23 HELIX 15 AB6 ASP A 512 LEU A 521 1 10 HELIX 16 AB7 ARG A 527 CYS A 532 1 6 HELIX 17 AB8 TYR A 598 SER A 603 1 6 HELIX 18 AB9 PRO A 634 THR A 639 1 6 HELIX 19 AC1 PRO A 674 PHE A 686 1 13 HELIX 20 AC2 ASP A 703 ASP A 717 1 15 HELIX 21 AC3 ARG A 768 ALA A 772 5 5 HELIX 22 AC4 SER A 801 LEU A 812 1 12 HELIX 23 AC5 THR A 889 GLN A 900 1 12 SHEET 1 AA1 4 ALA A 545 THR A 548 0 SHEET 2 AA1 4 TRP A 742 LEU A 745 1 O TRP A 742 N HIS A 546 SHEET 3 AA1 4 MET A 723 LYS A 725 -1 N VAL A 724 O LEU A 743 SHEET 4 AA1 4 THR A 564 GLU A 566 -1 N GLU A 566 O MET A 723 SHEET 1 AA2 4 VAL A 584 PHE A 587 0 SHEET 2 AA2 4 GLN A 572 ALA A 578 -1 N GLN A 575 O PHE A 587 SHEET 3 AA2 4 PHE A 616 ASP A 626 -1 O THR A 620 N ALA A 574 SHEET 4 AA2 4 GLN A 631 ILE A 632 -1 O GLN A 631 N ASP A 626 SHEET 1 AA3 5 VAL A 584 PHE A 587 0 SHEET 2 AA3 5 GLN A 572 ALA A 578 -1 N GLN A 575 O PHE A 587 SHEET 3 AA3 5 PHE A 616 ASP A 626 -1 O THR A 620 N ALA A 574 SHEET 4 AA3 5 GLN A 654 LEU A 665 -1 O GLN A 654 N TRP A 625 SHEET 5 AA3 5 GLU A 668 SER A 669 -1 O GLU A 668 N LEU A 665 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 LEU A 757 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 GLN A 791 N SER A 782 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 LEU A 757 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 O3' DT B 10 P 8GM B 11 1555 1555 1.61 LINK O3P AMP C 11 P DG C 12 1555 1555 1.56 CRYST1 64.122 115.579 125.679 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 0.015595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007957 0.00000 CONECT 4378 4390 CONECT 4390 4378 4391 4392 4393 CONECT 4391 4390 CONECT 4392 4390 CONECT 4393 4390 4394 CONECT 4394 4393 4395 CONECT 4395 4394 4396 4397 CONECT 4396 4395 4401 CONECT 4397 4395 4398 4399 CONECT 4398 4397 CONECT 4399 4397 4400 4401 CONECT 4400 4399 CONECT 4401 4396 4399 4402 CONECT 4402 4401 4403 4405 CONECT 4403 4402 4404 4413 CONECT 4404 4403 CONECT 4405 4402 4406 4412 CONECT 4406 4405 4407 CONECT 4407 4406 4408 4409 CONECT 4408 4407 CONECT 4409 4407 4410 CONECT 4410 4409 4411 4412 CONECT 4411 4410 CONECT 4412 4405 4410 4413 CONECT 4413 4403 4412 CONECT 4415 4416 4417 4418 4419 CONECT 4416 4415 CONECT 4417 4415 CONECT 4418 4415 4438 CONECT 4419 4415 4420 CONECT 4420 4419 4421 CONECT 4421 4420 4422 4423 CONECT 4422 4421 4427 CONECT 4423 4421 4424 4425 CONECT 4424 4423 CONECT 4425 4423 4426 4427 CONECT 4426 4425 CONECT 4427 4422 4425 4428 CONECT 4428 4427 4429 4437 CONECT 4429 4428 4430 CONECT 4430 4429 4431 CONECT 4431 4430 4432 4437 CONECT 4432 4431 4433 4434 CONECT 4433 4432 CONECT 4434 4432 4435 CONECT 4435 4434 4436 CONECT 4436 4435 4437 CONECT 4437 4428 4431 4436 CONECT 4438 4418 MASTER 525 0 2 23 26 0 0 6 4993 4 49 56 END