HEADER LIGASE/DNA 01-OCT-25 9YHX TITLE DNA LIGASE 1 E346A/E592A IN COMPLEX WITH NICK CONTAINING 3'-8OXODG:C TITLE 2 CAPTURED AT PRE-CATALYTIC STAGE CAVEAT 9YHX 8OG B 11 HAS WRONG CHIRALITY AT ATOM C3' 8OG B 11 HAS WRONG CAVEAT 2 9YHX CHIRALITY AT ATOM C1' 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*(8OG))-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 9YHX 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. 2.96 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) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 20007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1987 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 7.0800 - 5.6400 1.00 1337 147 0.2186 0.2459 REMARK 3 2 5.6400 - 4.9300 1.00 1303 145 0.1825 0.2408 REMARK 3 3 4.9300 - 4.4900 1.00 1311 146 0.1741 0.2209 REMARK 3 4 4.4800 - 4.1700 0.98 1270 143 0.1722 0.2049 REMARK 3 5 4.1700 - 3.9200 1.00 1300 135 0.1907 0.2619 REMARK 3 6 3.9200 - 3.7300 1.00 1270 147 0.2093 0.2895 REMARK 3 7 3.7300 - 3.5600 1.00 1282 147 0.2239 0.2834 REMARK 3 8 3.5600 - 3.4300 1.00 1281 135 0.2254 0.2891 REMARK 3 9 3.4300 - 3.3100 0.97 1231 136 0.2474 0.2886 REMARK 3 10 3.3100 - 3.2100 0.97 1237 129 0.2248 0.2772 REMARK 3 11 3.2100 - 3.1100 0.99 1287 150 0.2500 0.3068 REMARK 3 12 3.1100 - 3.0300 1.00 1262 150 0.2801 0.3511 REMARK 3 13 3.0300 - 2.9600 0.99 1266 126 0.3230 0.3869 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) : 27.580 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 : 0.003 5463 REMARK 3 ANGLE : 0.561 7608 REMARK 3 CHIRALITY : 0.037 883 REMARK 3 PLANARITY : 0.005 870 REMARK 3 DIHEDRAL : 18.161 1970 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): -5.6467 13.3303 -31.3325 REMARK 3 T TENSOR REMARK 3 T11: 0.6097 T22: 0.2605 REMARK 3 T33: 0.5438 T12: 0.0938 REMARK 3 T13: 0.0355 T23: 0.0649 REMARK 3 L TENSOR REMARK 3 L11: 1.6880 L22: 2.6088 REMARK 3 L33: 2.4774 L12: 0.0638 REMARK 3 L13: 0.1346 L23: 0.2142 REMARK 3 S TENSOR REMARK 3 S11: -0.2884 S12: -0.1575 S13: 0.0015 REMARK 3 S21: 0.1159 S22: 0.3333 S23: 0.1570 REMARK 3 S31: -0.0049 S32: -0.1540 S33: -0.0610 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 9YHX 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_1000300589. 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 : 6.2 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 : 20007 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.960 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.78900 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 (%): 54.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES(PH 6.2), 200 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 31.98350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.96100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.08650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.96100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.98350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.08650 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: 7500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 386 REMARK 465 ARG A 387 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 ASP A 751 REMARK 465 GLY A 754 REMARK 465 ILE A 908 REMARK 465 GLN A 909 REMARK 465 ASN A 910 REMARK 465 GLN A 911 REMARK 465 GLN A 912 REMARK 465 GLY A 913 REMARK 465 GLU A 914 REMARK 465 ASP A 915 REMARK 465 SER A 916 REMARK 465 GLY A 917 REMARK 465 SER A 918 REMARK 465 ASP A 919 REMARK 465 PRO A 920 REMARK 465 GLU A 921 REMARK 465 ASP A 922 REMARK 465 THR A 923 REMARK 465 ALA A 924 REMARK 465 ALA A 925 REMARK 465 ALA A 926 REMARK 465 LEU A 927 REMARK 465 GLU A 928 REMARK 465 HIS A 929 REMARK 465 HIS A 930 REMARK 465 HIS A 931 REMARK 465 HIS A 932 REMARK 465 HIS A 933 REMARK 465 HIS A 934 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 270 CE NZ REMARK 470 ASN A 271 CG OD1 ND2 REMARK 470 ASN A 272 CG OD1 ND2 REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 GLN A 285 CD OE1 NE2 REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 ARG A 364 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 365 CG CD OE1 NE2 REMARK 470 LEU A 366 CG CD1 CD2 REMARK 470 GLU A 367 CG CD OE1 OE2 REMARK 470 ARG A 370 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 GLU A 375 CG CD OE1 OE2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LEU A 381 CD1 CD2 REMARK 470 VAL A 382 CG1 CG2 REMARK 470 ASN A 385 CG OD1 ND2 REMARK 470 LEU A 394 CG CD1 CD2 REMARK 470 LYS A 422 CD CE NZ REMARK 470 LYS A 428 CD CE NZ REMARK 470 ARG A 435 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 440 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 475 CG CD OE1 OE2 REMARK 470 PRO A 478 CG CD REMARK 470 LYS A 485 CG CD CE NZ REMARK 470 LYS A 487 CG CD CE NZ REMARK 470 GLU A 490 CG CD OE1 OE2 REMARK 470 LYS A 493 CE NZ REMARK 470 GLU A 498 CG CD OE1 OE2 REMARK 470 ILE A 502 CD1 REMARK 470 ILE A 517 CD1 REMARK 470 ARG A 527 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 528 CD1 CD2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 ILE A 538 CD1 REMARK 470 HIS A 546 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 553 CD OE1 OE2 REMARK 470 VAL A 554 CG1 CG2 REMARK 470 LEU A 555 CD1 CD2 REMARK 470 LYS A 556 CG CD CE NZ REMARK 470 ARG A 557 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 559 CG CD OE1 OE2 REMARK 470 GLU A 560 CG CD OE1 OE2 REMARK 470 LYS A 568 CE NZ REMARK 470 LYS A 585 CE NZ REMARK 470 ILE A 586 CD1 REMARK 470 LYS A 597 NZ REMARK 470 ILE A 605 CD1 REMARK 470 LYS A 607 CG CD CE NZ REMARK 470 ILE A 608 CD1 REMARK 470 LYS A 609 CE NZ REMARK 470 ASP A 626 CG OD1 OD2 REMARK 470 ARG A 627 CG CD NE CZ NH1 NH2 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 ILE A 632 CG1 CG2 CD1 REMARK 470 LYS A 642 CG CD CE NZ 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 ILE A 651 CD1 REMARK 470 GLN A 652 CG CD OE1 NE2 REMARK 470 GLN A 654 CG CD OE1 NE2 REMARK 470 LEU A 662 CD1 CD2 REMARK 470 ILE A 663 CD1 REMARK 470 LEU A 665 CD1 CD2 REMARK 470 GLU A 668 CG CD OE1 OE2 REMARK 470 ARG A 672 CD NE CZ NH1 NH2 REMARK 470 LEU A 675 CG CD1 CD2 REMARK 470 GLN A 680 CG CD OE1 NE2 REMARK 470 LEU A 681 CD1 CD2 REMARK 470 ARG A 683 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 684 CG CD OE1 OE2 REMARK 470 VAL A 687 CG1 CG2 REMARK 470 GLU A 690 CG CD OE1 OE2 REMARK 470 GLU A 692 CD OE1 OE2 REMARK 470 VAL A 694 CG1 CG2 REMARK 470 LEU A 699 CG CD1 CD2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 ASP A 703 CG OD1 OD2 REMARK 470 ILE A 704 CD1 REMARK 470 GLU A 705 CG CD OE1 OE2 REMARK 470 ILE A 707 CG1 CG2 CD1 REMARK 470 GLU A 709 CG CD OE1 OE2 REMARK 470 LEU A 711 CG CD1 CD2 REMARK 470 GLU A 712 CG CD OE1 OE2 REMARK 470 SER A 714 OG REMARK 470 VAL A 715 CG1 CG2 REMARK 470 LYS A 716 CG CD CE NZ REMARK 470 SER A 718 OG REMARK 470 LEU A 722 CG CD1 CD2 REMARK 470 VAL A 724 CG1 CG2 REMARK 470 LEU A 727 CD1 CD2 REMARK 470 GLU A 734 CG CD OE1 OE2 REMARK 470 LYS A 737 CG CD CE NZ REMARK 470 ARG A 738 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 744 CG CD CE NZ REMARK 470 LEU A 745 CG CD1 CD2 REMARK 470 LYS A 747 CG CD CE NZ REMARK 470 VAL A 753 CG1 CG2 REMARK 470 ASP A 755 N CB CG OD1 OD2 REMARK 470 THR A 756 OG1 CG2 REMARK 470 VAL A 760 CG1 CG2 REMARK 470 GLU A 785 CG CD OE1 OE2 REMARK 470 SER A 787 OG REMARK 470 GLU A 788 CG CD OE1 OE2 REMARK 470 GLU A 806 CG CD OE1 OE2 REMARK 470 GLN A 810 CG CD OE1 NE2 REMARK 470 LEU A 812 CG CD1 CD2 REMARK 470 LYS A 813 CG CD CE NZ REMARK 470 VAL A 816 CG1 CG2 REMARK 470 ARG A 825 NE CZ NH1 NH2 REMARK 470 ILE A 826 CD1 REMARK 470 LEU A 836 CG CD1 CD2 REMARK 470 SER A 839 OG REMARK 470 LYS A 845 CD CE NZ REMARK 470 VAL A 878 CG1 CG2 REMARK 470 ARG A 879 NE CZ NH1 NH2 REMARK 470 GLU A 880 OE1 OE2 REMARK 470 LYS A 882 CE NZ REMARK 470 GLU A 885 CG CD OE1 OE2 REMARK 470 LYS A 904 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 262 OG SER A 264 2.07 REMARK 500 OP2 DG C 12 O HOH C 101 2.19 REMARK 500 N HIS A 274 OD2 ASP A 278 2.19 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 DT B 10 C3' - O3' - P ANGL. DEV. = -27.2 DEGREES REMARK 500 8OG B 11 O3' - P - OP2 ANGL. DEV. = 21.7 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 -125.55 62.84 REMARK 500 ALA A 455 -149.82 -133.21 REMARK 500 CYS A 532 95.28 -66.12 REMARK 500 PHE A 558 43.00 -94.32 REMARK 500 GLU A 580 97.71 -67.72 REMARK 500 LEU A 665 114.71 -160.18 REMARK 500 ASP A 728 -53.78 -134.71 REMARK 500 TYR A 733 47.90 -87.11 REMARK 500 LYS A 737 -70.94 -67.60 REMARK 500 LYS A 770 2.53 -66.16 REMARK 500 ASP A 827 -137.66 57.92 REMARK 500 PRO A 838 94.25 -68.46 REMARK 500 SER A 839 13.78 -149.75 REMARK 500 ILE A 876 -61.44 -123.50 REMARK 500 GLN A 886 59.35 -95.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YHX A 262 923 UNP P18858 DNLI1_HUMAN 262 918 DBREF 9YHX B 1 11 PDB 9YHX 9YHX 1 11 DBREF 9YHX C 11 18 PDB 9YHX 9YHX 11 18 DBREF 9YHX D 1 18 PDB 9YHX 9YHX 1 18 SEQADV 9YHX ALA A 346 UNP P18858 GLU 346 ENGINEERED MUTATION SEQADV 9YHX ALA A 592 UNP P18858 GLU 592 ENGINEERED MUTATION SEQADV 9YHX ALA A 924 UNP P18858 EXPRESSION TAG SEQADV 9YHX ALA A 925 UNP P18858 EXPRESSION TAG SEQADV 9YHX ALA A 926 UNP P18858 EXPRESSION TAG SEQADV 9YHX LEU A 927 UNP P18858 EXPRESSION TAG SEQADV 9YHX GLU A 928 UNP P18858 EXPRESSION TAG SEQADV 9YHX HIS A 929 UNP P18858 EXPRESSION TAG SEQADV 9YHX HIS A 930 UNP P18858 EXPRESSION TAG SEQADV 9YHX HIS A 931 UNP P18858 EXPRESSION TAG SEQADV 9YHX HIS A 932 UNP P18858 EXPRESSION TAG SEQADV 9YHX HIS A 933 UNP P18858 EXPRESSION TAG SEQADV 9YHX HIS A 934 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 8OG 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 8OG B 11 23 HET AMP C 11 22 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 3 AMP C10 H14 N5 O7 P FORMUL 5 HOH *19(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 ALA A 433 1 16 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 GLY A 550 PHE A 558 1 9 HELIX 16 AB7 TYR A 598 ILE A 605 1 8 HELIX 17 AB8 PRO A 634 THR A 639 1 6 HELIX 18 AB9 PRO A 674 PHE A 686 1 13 HELIX 19 AC1 ASP A 703 ASP A 717 1 15 HELIX 20 AC2 ASP A 748 LEU A 750 5 3 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 905 1 12 SHEET 1 AA1 5 ALA A 545 PRO A 547 0 SHEET 2 AA1 5 TRP A 742 LYS A 746 1 O LYS A 744 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 LYS A 568 -1 N GLU A 566 O MET A 723 SHEET 5 AA1 5 SER A 698 LEU A 699 -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 GLN A 654 LEU A 665 -1 O GLN A 654 N TRP A 625 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 GLN A 654 LEU A 665 -1 O GLN A 654 N TRP A 625 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 LEU A 796 N PHE A 778 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 GLY A 867 N SER A 852 LINK O3' DT B 10 P 8OG B 11 1555 1555 1.56 CISPEP 1 PHE A 476 PRO A 477 0 -3.15 CRYST1 63.967 116.173 125.922 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 0.015633 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007941 0.00000 CONECT 4718 4730 CONECT 4730 4718 4731 4732 4733 CONECT 4731 4730 CONECT 4732 4730 CONECT 4733 4730 4734 CONECT 4734 4733 4735 CONECT 4735 4734 4736 4737 CONECT 4736 4735 4740 CONECT 4737 4735 4738 4739 CONECT 4738 4737 CONECT 4739 4737 4740 CONECT 4740 4736 4739 4741 CONECT 4741 4740 4742 4751 CONECT 4742 4741 4743 4752 CONECT 4743 4742 4744 CONECT 4744 4743 4745 4751 CONECT 4745 4744 4746 4747 CONECT 4746 4745 CONECT 4747 4745 4748 CONECT 4748 4747 4749 4750 CONECT 4749 4748 CONECT 4750 4748 4751 CONECT 4751 4741 4744 4750 CONECT 4752 4742 CONECT 4754 4755 4756 4757 CONECT 4755 4754 CONECT 4756 4754 CONECT 4757 4754 4758 CONECT 4758 4757 4759 CONECT 4759 4758 4760 4761 CONECT 4760 4759 4765 CONECT 4761 4759 4762 4763 CONECT 4762 4761 CONECT 4763 4761 4764 4765 CONECT 4764 4763 CONECT 4765 4760 4763 4766 CONECT 4766 4765 4767 4775 CONECT 4767 4766 4768 CONECT 4768 4767 4769 CONECT 4769 4768 4770 4775 CONECT 4770 4769 4771 4772 CONECT 4771 4770 CONECT 4772 4770 4773 CONECT 4773 4772 4774 CONECT 4774 4773 4775 CONECT 4775 4766 4769 4774 MASTER 462 0 2 23 27 0 0 6 5295 4 46 56 END