HEADER LIGASE/DNA 01-OCT-25 9YHU TITLE DNA LIGASE 1 E346A/E592A IN COMPLEX WITH NICK CONTAINING 3'-8OXORG:A TITLE 2 CAPTURED AT POST-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) COMPND 10 P*GP*TP*CP*GP*GP*AP*C)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'- COMPND 15 D(P*GP*TP*CP*CP*GP*AP*CP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 16 CHAIN: C; COMPND 17 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 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 9YHU 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 63680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 24.5600 - 4.7100 0.98 4624 149 0.1487 0.1566 REMARK 3 2 4.7100 - 3.7400 0.99 4498 147 0.1389 0.1654 REMARK 3 3 3.7400 - 3.2700 1.00 4492 145 0.1702 0.2169 REMARK 3 4 3.2700 - 2.9700 0.97 4322 140 0.1934 0.2296 REMARK 3 5 2.9700 - 2.7600 0.99 4412 143 0.2020 0.2316 REMARK 3 6 2.7600 - 2.6000 1.00 4440 144 0.2017 0.2345 REMARK 3 7 2.6000 - 2.4700 1.00 4409 143 0.1912 0.2179 REMARK 3 8 2.4700 - 2.3600 1.00 4424 144 0.1827 0.2211 REMARK 3 9 2.3600 - 2.2700 1.00 4363 141 0.1827 0.2458 REMARK 3 10 2.2700 - 2.1900 0.97 4283 139 0.1773 0.1972 REMARK 3 11 2.1900 - 2.1200 0.97 4286 139 0.1770 0.2251 REMARK 3 12 2.1200 - 2.0600 1.00 4395 142 0.1755 0.2209 REMARK 3 13 2.0600 - 2.0100 1.00 4380 141 0.1834 0.2235 REMARK 3 14 2.0100 - 1.9600 0.99 4353 142 0.1984 0.2491 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.560 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 : 0.010 5736 REMARK 3 ANGLE : 1.107 7954 REMARK 3 CHIRALITY : 0.063 911 REMARK 3 PLANARITY : 0.011 902 REMARK 3 DIHEDRAL : 20.747 2196 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): -20.1904 4.2920 -10.7226 REMARK 3 T TENSOR REMARK 3 T11: 0.1867 T22: 0.1779 REMARK 3 T33: 0.1704 T12: 0.0204 REMARK 3 T13: 0.0067 T23: -0.0213 REMARK 3 L TENSOR REMARK 3 L11: 0.9591 L22: 0.6959 REMARK 3 L33: 0.5270 L12: 0.1551 REMARK 3 L13: 0.1522 L23: -0.0075 REMARK 3 S TENSOR REMARK 3 S11: 0.0166 S12: 0.0096 S13: -0.0343 REMARK 3 S21: 0.0406 S22: 0.0031 S23: -0.0393 REMARK 3 S31: 0.0220 S32: -0.0492 S33: -0.0200 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 9YHU 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_1000300592. 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 : 6.5 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 : 121298 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23800 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 (%): 52.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES (PH 6.5), 200 MM LITHIUM REMARK 280 ACETATE, 12% (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 37.33400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.00200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.97050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.00200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.33400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.97050 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 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 LEU A 394 REMARK 465 GLY A 754 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 LYS A 282 NZ REMARK 470 LYS A 286 NZ REMARK 470 ARG A 305 CZ NH1 NH2 REMARK 470 LEU A 306 CD1 REMARK 470 GLU A 310 OE1 OE2 REMARK 470 LEU A 345 CD2 REMARK 470 LYS A 356 CD CE NZ REMARK 470 ALA A 359 CB REMARK 470 GLN A 365 CG CD OE1 NE2 REMARK 470 GLU A 367 CG CD OE1 OE2 REMARK 470 ARG A 370 CD NE CZ NH1 NH2 REMARK 470 GLU A 375 CG CD OE1 OE2 REMARK 470 LYS A 376 CD CE NZ REMARK 470 LEU A 381 CG CD1 CD2 REMARK 470 ASN A 385 OD1 ND2 REMARK 470 SER A 386 OG REMARK 470 LYS A 422 CE NZ REMARK 470 LYS A 428 NZ REMARK 470 ARG A 435 CZ NH1 NH2 REMARK 470 GLU A 475 CG CD OE1 OE2 REMARK 470 LYS A 485 CG CD CE NZ REMARK 470 GLU A 490 CG CD OE1 OE2 REMARK 470 LYS A 493 CD CE NZ REMARK 470 GLN A 505 CG CD OE1 NE2 REMARK 470 GLU A 526 CG CD OE1 OE2 REMARK 470 ARG A 527 CD NE CZ NH1 NH2 REMARK 470 LYS A 533 CD CE NZ REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 553 CG CD OE1 OE2 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 585 NZ REMARK 470 GLU A 628 OE1 OE2 REMARK 470 LYS A 629 CE NZ REMARK 470 LYS A 630 CE NZ REMARK 470 ARG A 643 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 644 CE NZ 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 ARG A 672 CD NE CZ NH1 NH2 REMARK 470 GLU A 690 CD OE1 OE2 REMARK 470 LYS A 702 CE NZ REMARK 470 ILE A 704 CD1 REMARK 470 GLU A 705 CG CD OE1 OE2 REMARK 470 LYS A 737 CE NZ REMARK 470 LYS A 747 CE NZ REMARK 470 ASP A 751 CG OD1 OD2 REMARK 470 ASP A 755 N CA CB CG OD1 OD2 REMARK 470 LYS A 813 CG CD CE NZ REMARK 470 ARG A 825 CZ NH1 NH2 REMARK 470 GLU A 880 CD OE1 OE2 REMARK 470 LYS A 899 CD CE NZ REMARK 470 GLN A 902 CG CD OE1 NE2 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 OP2 DC C 15 O HOH C 101 2.02 REMARK 500 OP2 DG B 7 O HOH B 101 2.09 REMARK 500 O HOH A 1104 O HOH A 1391 2.13 REMARK 500 OD1 ASP A 848 O HOH A 1101 2.14 REMARK 500 NE2 GLN A 343 O HOH A 1102 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 15 O3' DC C 15 C3' -0.039 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 12 O5' - P - OP1 ANGL. DEV. = 11.0 DEGREES REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC C 10 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG C 11 O5' - P - OP1 ANGL. DEV. = 11.4 DEGREES REMARK 500 DG C 11 O5' - P - OP2 ANGL. DEV. = -6.7 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 ASN A 385 41.29 -81.99 REMARK 500 HIS A 436 -117.76 49.75 REMARK 500 ALA A 455 -145.84 -137.78 REMARK 500 ARG A 549 37.08 -98.69 REMARK 500 GLU A 559 -114.71 52.67 REMARK 500 GLU A 692 -50.38 -131.19 REMARK 500 HIS A 740 57.53 -114.20 REMARK 500 ASP A 827 -114.05 39.39 REMARK 500 SER A 839 -49.71 -154.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 9YHU A 262 918 UNP P18858 DNLI1_HUMAN 262 918 DBREF 9YHU B 1 18 PDB 9YHU 9YHU 1 18 DBREF 9YHU C 1 18 PDB 9YHU 9YHU 1 18 SEQADV 9YHU ALA A 346 UNP P18858 GLU 346 ENGINEERED MUTATION SEQADV 9YHU ALA A 592 UNP P18858 GLU 592 ENGINEERED MUTATION SEQADV 9YHU ALA A 919 UNP P18858 EXPRESSION TAG SEQADV 9YHU ALA A 920 UNP P18858 EXPRESSION TAG SEQADV 9YHU ALA A 921 UNP P18858 EXPRESSION TAG SEQADV 9YHU LEU A 922 UNP P18858 EXPRESSION TAG SEQADV 9YHU GLU A 923 UNP P18858 EXPRESSION TAG SEQADV 9YHU HIS A 924 UNP P18858 EXPRESSION TAG SEQADV 9YHU HIS A 925 UNP P18858 EXPRESSION TAG SEQADV 9YHU HIS A 926 UNP P18858 EXPRESSION TAG SEQADV 9YHU HIS A 927 UNP P18858 EXPRESSION TAG SEQADV 9YHU HIS A 928 UNP P18858 EXPRESSION TAG SEQADV 9YHU 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 18 DG DC DT DG DA DT DG DC DG DT 8GM DG DT SEQRES 2 B 18 DC DG DG DA DC SEQRES 1 C 18 DG DT DC DC DG DA DC DA DA DC DG DC DA SEQRES 2 C 18 DT DC DA DG DC HET 8GM B 11 24 HET AMP A1001 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 4 AMP C10 H14 N5 O7 P FORMUL 5 HOH *428(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 GLY A 448 1 12 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 LYS A 746 LEU A 750 5 5 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 SER A 901 1 13 SHEET 1 AA1 5 ALA A 545 PRO A 547 0 SHEET 2 AA1 5 TRP A 742 LEU A 745 1 O TRP A 742 N HIS A 546 SHEET 3 AA1 5 LEU A 722 THR A 726 -1 N VAL A 724 O LEU A 743 SHEET 4 AA1 5 PHE A 563 TYR A 567 -1 N THR A 564 O LYS A 725 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 TYR A 658 N GLU A 621 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 TYR A 658 N GLU A 621 SHEET 4 AA3 4 PHE A 693 PHE A 695 1 O VAL A 694 N ALA A 659 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 LEU A 779 N ILE A 762 SHEET 5 AA4 6 GLU A 789 LEU A 796 -1 O CYS A 794 N LEU A 780 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 GLY A 867 N SER A 852 LINK O3' DT B 10 P 8GM B 11 1555 1555 1.60 LINK O3' 8GM B 11 P DG B 12 1555 1555 1.62 CISPEP 1 PHE A 476 PRO A 477 0 -2.50 CRYST1 74.668 101.941 116.004 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 0.013393 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008620 0.00000 CONECT 4980 4992 CONECT 4992 4980 4993 4994 4995 CONECT 4993 4992 CONECT 4994 4992 CONECT 4995 4992 4996 CONECT 4996 4995 4997 CONECT 4997 4996 4998 4999 CONECT 4998 4997 5003 CONECT 4999 4997 5000 5001 CONECT 5000 4999 5016 CONECT 5001 4999 5002 5003 CONECT 5002 5001 CONECT 5003 4998 5001 5004 CONECT 5004 5003 5005 5007 CONECT 5005 5004 5006 5015 CONECT 5006 5005 CONECT 5007 5004 5008 5014 CONECT 5008 5007 5009 CONECT 5009 5008 5010 5011 CONECT 5010 5009 CONECT 5011 5009 5012 CONECT 5012 5011 5013 5014 CONECT 5013 5012 CONECT 5014 5007 5012 5015 CONECT 5015 5005 5014 CONECT 5016 5000 CONECT 5526 5527 5528 5529 5530 CONECT 5527 5526 CONECT 5528 5526 CONECT 5529 5526 CONECT 5530 5526 5531 CONECT 5531 5530 5532 CONECT 5532 5531 5533 5534 CONECT 5533 5532 5538 CONECT 5534 5532 5535 5536 CONECT 5535 5534 CONECT 5536 5534 5537 5538 CONECT 5537 5536 CONECT 5538 5533 5536 5539 CONECT 5539 5538 5540 5548 CONECT 5540 5539 5541 CONECT 5541 5540 5542 CONECT 5542 5541 5543 5548 CONECT 5543 5542 5544 5545 CONECT 5544 5543 CONECT 5545 5543 5546 CONECT 5546 5545 5547 CONECT 5547 5546 5548 CONECT 5548 5539 5542 5547 MASTER 409 0 2 27 27 0 0 6 5952 3 49 56 END