HEADER LIGASE/DNA 08-NOV-17 6BKG TITLE HUMAN LIGIV CATALYTIC DOMAIN WITH BOUND DNA-ADENYLATE INTERMEDIATE IN TITLE 2 CLOSED CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA LIGASE IV,POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] 4; COMPND 5 EC: 6.5.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'); COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 14 CHAIN: T; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*(AMP)P*GP*TP*CP*GP*GP*AP*C)-3'); COMPND 18 CHAIN: D; COMPND 19 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: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS DNA DOUBLE-STRAND BREAK REPAIR, LIGASE, NONHOMOLOGOUS END-JOINING, KEYWDS 2 LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.F.MOON,P.P.TUMBALE,M.J.SCHELLENBERG,R.S.WILLIAMS,J.G.WILLIAMS, AUTHOR 2 T.A.KUNKEL,L.C.PEDERSEN,B.BEBENEK REVDAT 5 04-OCT-23 6BKG 1 LINK REVDAT 4 18-DEC-19 6BKG 1 REMARK REVDAT 3 17-JUL-19 6BKG 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES LINK SITE ATOM REVDAT 2 20-FEB-19 6BKG 1 REMARK REVDAT 1 18-JUL-18 6BKG 0 JRNL AUTH A.M.KAMINSKI,P.P.TUMBALE,M.J.SCHELLENBERG,R.S.WILLIAMS, JRNL AUTH 2 J.G.WILLIAMS,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK JRNL TITL STRUCTURES OF DNA-BOUND HUMAN LIGASE IV CATALYTIC CORE JRNL TITL 2 REVEAL INSIGHTS INTO SUBSTRATE BINDING AND CATALYSIS. JRNL REF NAT COMMUN V. 9 2642 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29980672 JRNL DOI 10.1038/S41467-018-05024-8 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 32630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1626 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 39.2051 - 5.4943 1.00 2760 150 0.1844 0.2216 REMARK 3 2 5.4943 - 4.3629 1.00 2645 135 0.1614 0.1829 REMARK 3 3 4.3629 - 3.8119 1.00 2613 141 0.1623 0.2234 REMARK 3 4 3.8119 - 3.4636 1.00 2629 129 0.1853 0.2280 REMARK 3 5 3.4636 - 3.2155 1.00 2559 144 0.1966 0.2275 REMARK 3 6 3.2155 - 3.0260 1.00 2598 131 0.2191 0.2693 REMARK 3 7 3.0260 - 2.8745 1.00 2578 141 0.2471 0.3025 REMARK 3 8 2.8745 - 2.7494 1.00 2554 131 0.2573 0.3008 REMARK 3 9 2.7494 - 2.6436 1.00 2582 134 0.2604 0.3021 REMARK 3 10 2.6436 - 2.5524 1.00 2571 132 0.2686 0.3009 REMARK 3 11 2.5524 - 2.4726 1.00 2539 142 0.2659 0.3260 REMARK 3 12 2.4726 - 2.4019 0.93 2376 116 0.2678 0.3724 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.700 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 5602 REMARK 3 ANGLE : 0.585 7738 REMARK 3 CHIRALITY : 0.040 875 REMARK 3 PLANARITY : 0.004 852 REMARK 3 DIHEDRAL : 13.756 3253 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 7:237) REMARK 3 ORIGIN FOR THE GROUP (A): -34.3609 -7.4433 19.1284 REMARK 3 T TENSOR REMARK 3 T11: 0.2293 T22: 0.3096 REMARK 3 T33: 0.4475 T12: -0.0228 REMARK 3 T13: 0.0232 T23: 0.0316 REMARK 3 L TENSOR REMARK 3 L11: 2.1503 L22: 2.3059 REMARK 3 L33: 2.1052 L12: -0.5957 REMARK 3 L13: 0.1599 L23: -0.5234 REMARK 3 S TENSOR REMARK 3 S11: -0.0145 S12: -0.2392 S13: -0.3110 REMARK 3 S21: 0.0386 S22: 0.0164 S23: 0.5038 REMARK 3 S31: 0.1234 S32: -0.1842 S33: 0.0051 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 238:458) REMARK 3 ORIGIN FOR THE GROUP (A): -1.1071 -19.4089 14.9608 REMARK 3 T TENSOR REMARK 3 T11: 0.3106 T22: 0.2885 REMARK 3 T33: 0.3827 T12: 0.0549 REMARK 3 T13: -0.0026 T23: 0.0202 REMARK 3 L TENSOR REMARK 3 L11: 1.6327 L22: 3.3275 REMARK 3 L33: 0.9636 L12: 0.4668 REMARK 3 L13: -0.3526 L23: 0.1801 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: 0.0944 S13: -0.0572 REMARK 3 S21: -0.0214 S22: 0.0702 S23: -0.2089 REMARK 3 S31: 0.1679 S32: 0.1197 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 459:616) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2189 15.6920 8.5474 REMARK 3 T TENSOR REMARK 3 T11: 0.3336 T22: 0.3342 REMARK 3 T33: 0.3470 T12: -0.0104 REMARK 3 T13: 0.0743 T23: 0.0898 REMARK 3 L TENSOR REMARK 3 L11: 2.6484 L22: 2.9065 REMARK 3 L33: 0.7560 L12: 0.2012 REMARK 3 L13: 0.6644 L23: -0.3199 REMARK 3 S TENSOR REMARK 3 S11: 0.0723 S12: 0.2963 S13: 0.5295 REMARK 3 S21: -0.4383 S22: -0.1046 S23: -0.2585 REMARK 3 S31: -0.0470 S32: 0.1372 S33: -0.0052 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN T AND RESID 1:7) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6503 -0.9565 24.6276 REMARK 3 T TENSOR REMARK 3 T11: 0.6264 T22: 0.4622 REMARK 3 T33: 0.2514 T12: 0.0211 REMARK 3 T13: -0.0560 T23: 0.0518 REMARK 3 L TENSOR REMARK 3 L11: 0.5703 L22: 1.7460 REMARK 3 L33: 2.1353 L12: 0.4776 REMARK 3 L13: -0.2745 L23: -1.8577 REMARK 3 S TENSOR REMARK 3 S11: 0.4309 S12: -0.4446 S13: 0.0692 REMARK 3 S21: 0.2649 S22: 0.6508 S23: 0.6237 REMARK 3 S31: 1.2681 S32: -0.4043 S33: 0.2481 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN T AND RESID 8:18) REMARK 3 ORIGIN FOR THE GROUP (A): -18.5597 -1.6816 -3.1554 REMARK 3 T TENSOR REMARK 3 T11: 0.4509 T22: 0.5808 REMARK 3 T33: 0.2456 T12: 0.0660 REMARK 3 T13: 0.0098 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.3083 L22: 0.5773 REMARK 3 L33: 0.3153 L12: 0.0704 REMARK 3 L13: 0.1572 L23: -0.4453 REMARK 3 S TENSOR REMARK 3 S11: 0.0738 S12: 0.6709 S13: -0.0729 REMARK 3 S21: -0.2511 S22: 0.2233 S23: -0.0126 REMARK 3 S31: -0.3277 S32: -0.0078 S33: 0.0092 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN P AND RESID 1:11) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1717 -1.7941 -1.3025 REMARK 3 T TENSOR REMARK 3 T11: 0.5280 T22: 0.4954 REMARK 3 T33: 0.2535 T12: -0.0161 REMARK 3 T13: -0.0556 T23: -0.0373 REMARK 3 L TENSOR REMARK 3 L11: 1.1178 L22: 0.0123 REMARK 3 L33: 0.0203 L12: -0.1906 REMARK 3 L13: -0.0920 L23: 0.0451 REMARK 3 S TENSOR REMARK 3 S11: 0.1877 S12: 0.6339 S13: -0.7163 REMARK 3 S21: -0.2532 S22: 0.0906 S23: 0.0477 REMARK 3 S31: -0.4755 S32: 0.5710 S33: 0.0022 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN D AND RESID 2:8) REMARK 3 ORIGIN FOR THE GROUP (A): -10.9888 1.9889 23.9755 REMARK 3 T TENSOR REMARK 3 T11: 0.4384 T22: 0.3415 REMARK 3 T33: 0.2155 T12: -0.0372 REMARK 3 T13: 0.0279 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 0.3692 L22: 0.4029 REMARK 3 L33: 0.6144 L12: 0.0142 REMARK 3 L13: 0.0522 L23: 0.1291 REMARK 3 S TENSOR REMARK 3 S11: 0.2576 S12: -0.6164 S13: 0.1953 REMARK 3 S21: 0.6188 S22: 0.3204 S23: -0.2063 REMARK 3 S31: 0.2547 S32: 0.1878 S33: 0.0528 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 6BKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000231024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR REMARK 200 HIGH-RESOLUTION DOUBLE-CRYSTAL REMARK 200 SI(220) SAGITTAL FOCUSING REMARK 200 OPTICS : ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32742 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 31.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.84600 REMARK 200 FOR SHELL : 2.450 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3W5O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 78.2MM HEPES PH 7.5, 15.64% PEG4000, REMARK 280 7.82% ISOPROPANOL, 13.8% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 36.32850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.06550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.37350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.06550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.32850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.37350 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: 7490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T, 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 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 THR A 6 REMARK 465 HIS A 57 REMARK 465 LYS A 58 REMARK 465 GLY A 117 REMARK 465 THR A 118 REMARK 465 HIS A 119 REMARK 465 LEU A 138 REMARK 465 VAL A 355 REMARK 465 GLU A 356 REMARK 465 ASP A 357 REMARK 465 SER A 358 REMARK 465 ILE A 617 REMARK 465 GLY A 618 REMARK 465 GLY A 619 REMARK 465 ASP A 620 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 SER A 7 OG REMARK 470 GLN A 8 CD OE1 NE2 REMARK 470 LYS A 28 CE NZ REMARK 470 LYS A 30 CG CD CE NZ REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ASN A 56 CG OD1 ND2 REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 VAL A 60 CG1 CG2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 GLN A 139 CG CD OE1 NE2 REMARK 470 LYS A 140 NZ REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 LYS A 169 CD CE NZ REMARK 470 LYS A 223 CD CE NZ REMARK 470 ARG A 226 CZ NH1 NH2 REMARK 470 ASP A 237 CG OD1 OD2 REMARK 470 LYS A 247 CE NZ REMARK 470 ASP A 255 CG OD1 OD2 REMARK 470 GLU A 257 CG CD OE1 OE2 REMARK 470 LYS A 261 CD CE NZ REMARK 470 LYS A 264 CE NZ REMARK 470 ASP A 300 OD1 OD2 REMARK 470 ASN A 338 CG OD1 ND2 REMARK 470 GLN A 340 OE1 NE2 REMARK 470 MET A 343 CG SD CE REMARK 470 LYS A 348 CG CD CE NZ REMARK 470 ARG A 353 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 359 CG OD1 OD2 REMARK 470 ASN A 374 CG OD1 ND2 REMARK 470 LYS A 375 CD CE NZ REMARK 470 ILE A 392 CD1 REMARK 470 GLN A 404 CG CD OE1 NE2 REMARK 470 GLN A 407 CG CD OE1 NE2 REMARK 470 HIS A 409 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 411 CD CE NZ REMARK 470 GLU A 420 CD OE1 OE2 REMARK 470 LYS A 424 CE NZ REMARK 470 LYS A 442 CG CD CE NZ REMARK 470 GLU A 445 CD OE1 OE2 REMARK 470 SER A 456 OG REMARK 470 LEU A 458 CD1 CD2 REMARK 470 LYS A 473 NZ REMARK 470 LYS A 490 CG CD CE NZ REMARK 470 GLU A 495 CG CD OE1 OE2 REMARK 470 LYS A 496 NZ REMARK 470 LYS A 513 CE NZ REMARK 470 LYS A 524 NZ REMARK 470 LYS A 527 CE NZ REMARK 470 ARG A 531 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 532 CG CD CE NZ REMARK 470 ASP A 568 CG OD1 OD2 REMARK 470 LYS A 583 NZ REMARK 470 LYS A 588 CE NZ REMARK 470 ASP A 597 CG OD1 OD2 REMARK 470 GLU A 600 CG CD OE1 OE2 REMARK 470 GLN A 601 OE1 NE2 REMARK 470 LYS A 613 CE NZ REMARK 470 TYR A 616 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 DC P 11 O3' 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 LYS A 55 -56.25 60.86 REMARK 500 VAL A 60 126.04 78.56 REMARK 500 LYS A 85 -154.40 -121.76 REMARK 500 LYS A 192 48.01 70.93 REMARK 500 ASP A 237 67.11 -118.31 REMARK 500 HIS A 265 16.59 56.31 REMARK 500 PRO A 306 2.91 -67.66 REMARK 500 LEU A 311 -49.02 -135.95 REMARK 500 LYS A 348 -7.52 78.43 REMARK 500 ARG A 353 70.35 -161.05 REMARK 500 ARG A 353 68.96 -161.05 REMARK 500 ASN A 373 -119.30 54.52 REMARK 500 ARG A 399 -50.82 -131.27 REMARK 500 ALA A 533 62.86 -155.10 REMARK 500 ALA A 606 51.06 -155.08 REMARK 500 SER A 612 25.24 -146.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 509 O REMARK 620 2 HOH A 801 O 80.8 REMARK 620 3 HOH A 808 O 63.2 73.4 REMARK 620 4 HOH A 864 O 109.6 119.2 165.5 REMARK 620 5 DG D 5 OP1 84.6 142.8 69.5 97.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP D 101 DBREF 6BKG A 1 620 UNP P49917 DNLI4_HUMAN 1 620 DBREF 6BKG P 1 11 PDB 6BKG 6BKG 1 11 DBREF 6BKG T 1 18 PDB 6BKG 6BKG 1 18 DBREF 6BKG D 2 8 PDB 6BKG 6BKG 2 8 SEQADV 6BKG THR A 0 UNP P49917 EXPRESSION TAG SEQRES 1 A 621 THR MET ALA ALA SER GLN THR SER GLN THR VAL ALA SER SEQRES 2 A 621 HIS VAL PRO PHE ALA ASP LEU CYS SER THR LEU GLU ARG SEQRES 3 A 621 ILE GLN LYS SER LYS GLY ARG ALA GLU LYS ILE ARG HIS SEQRES 4 A 621 PHE ARG GLU PHE LEU ASP SER TRP ARG LYS PHE HIS ASP SEQRES 5 A 621 ALA LEU HIS LYS ASN HIS LYS ASP VAL THR ASP SER PHE SEQRES 6 A 621 TYR PRO ALA MET ARG LEU ILE LEU PRO GLN LEU GLU ARG SEQRES 7 A 621 GLU ARG MET ALA TYR GLY ILE LYS GLU THR MET LEU ALA SEQRES 8 A 621 LYS LEU TYR ILE GLU LEU LEU ASN LEU PRO ARG ASP GLY SEQRES 9 A 621 LYS ASP ALA LEU LYS LEU LEU ASN TYR ARG THR PRO THR SEQRES 10 A 621 GLY THR HIS GLY ASP ALA GLY ASP PHE ALA MET ILE ALA SEQRES 11 A 621 TYR PHE VAL LEU LYS PRO ARG CYS LEU GLN LYS GLY SER SEQRES 12 A 621 LEU THR ILE GLN GLN VAL ASN ASP LEU LEU ASP SER ILE SEQRES 13 A 621 ALA SER ASN ASN SER ALA LYS ARG LYS ASP LEU ILE LYS SEQRES 14 A 621 LYS SER LEU LEU GLN LEU ILE THR GLN SER SER ALA LEU SEQRES 15 A 621 GLU GLN LYS TRP LEU ILE ARG MET ILE ILE LYS ASP LEU SEQRES 16 A 621 LYS LEU GLY VAL SER GLN GLN THR ILE PHE SER VAL PHE SEQRES 17 A 621 HIS ASN ASP ALA ALA GLU LEU HIS ASN VAL THR THR ASP SEQRES 18 A 621 LEU GLU LYS VAL CYS ARG GLN LEU HIS ASP PRO SER VAL SEQRES 19 A 621 GLY LEU SER ASP ILE SER ILE THR LEU PHE SER ALA PHE SEQRES 20 A 621 LYS PRO MET LEU ALA ALA ILE ALA ASP ILE GLU HIS ILE SEQRES 21 A 621 GLU LYS ASP MET LYS HIS GLN SER PHE TYR ILE GLU THR SEQRES 22 A 621 LYS LEU ASP GLY GLU ARG MET GLN MET HIS LYS ASP GLY SEQRES 23 A 621 ASP VAL TYR LYS TYR PHE SER ARG ASN GLY TYR ASN TYR SEQRES 24 A 621 THR ASP GLN PHE GLY ALA SER PRO THR GLU GLY SER LEU SEQRES 25 A 621 THR PRO PHE ILE HIS ASN ALA PHE LYS ALA ASP ILE GLN SEQRES 26 A 621 ILE CYS ILE LEU ASP GLY GLU MET MET ALA TYR ASN PRO SEQRES 27 A 621 ASN THR GLN THR PHE MET GLN LYS GLY THR LYS PHE ASP SEQRES 28 A 621 ILE LYS ARG MET VAL GLU ASP SER ASP LEU GLN THR CYS SEQRES 29 A 621 TYR CYS VAL PHE ASP VAL LEU MET VAL ASN ASN LYS LYS SEQRES 30 A 621 LEU GLY HIS GLU THR LEU ARG LYS ARG TYR GLU ILE LEU SEQRES 31 A 621 SER SER ILE PHE THR PRO ILE PRO GLY ARG ILE GLU ILE SEQRES 32 A 621 VAL GLN LYS THR GLN ALA HIS THR LYS ASN GLU VAL ILE SEQRES 33 A 621 ASP ALA LEU ASN GLU ALA ILE ASP LYS ARG GLU GLU GLY SEQRES 34 A 621 ILE MET VAL LYS GLN PRO LEU SER ILE TYR LYS PRO ASP SEQRES 35 A 621 LYS ARG GLY GLU GLY TRP LEU LYS ILE LYS PRO GLU TYR SEQRES 36 A 621 VAL SER GLY LEU MET ASP GLU LEU ASP ILE LEU ILE VAL SEQRES 37 A 621 GLY GLY TYR TRP GLY LYS GLY SER ARG GLY GLY MET MET SEQRES 38 A 621 SER HIS PHE LEU CYS ALA VAL ALA GLU LYS PRO PRO PRO SEQRES 39 A 621 GLY GLU LYS PRO SER VAL PHE HIS THR LEU SER ARG VAL SEQRES 40 A 621 GLY SER GLY CYS THR MET LYS GLU LEU TYR ASP LEU GLY SEQRES 41 A 621 LEU LYS LEU ALA LYS TYR TRP LYS PRO PHE HIS ARG LYS SEQRES 42 A 621 ALA PRO PRO SER SER ILE LEU CYS GLY THR GLU LYS PRO SEQRES 43 A 621 GLU VAL TYR ILE GLU PRO CYS ASN SER VAL ILE VAL GLN SEQRES 44 A 621 ILE LYS ALA ALA GLU ILE VAL PRO SER ASP MET TYR LYS SEQRES 45 A 621 THR GLY CYS THR LEU ARG PHE PRO ARG ILE GLU LYS ILE SEQRES 46 A 621 ARG ASP ASP LYS GLU TRP HIS GLU CYS MET THR LEU ASP SEQRES 47 A 621 ASP LEU GLU GLN LEU ARG GLY LYS ALA SER GLY LYS LEU SEQRES 48 A 621 ALA SER LYS HIS LEU TYR ILE GLY GLY ASP SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG DT DC SEQRES 1 T 18 DG DT DC DC DG DA DC DG DA DC DG DC DA SEQRES 2 T 18 DT DC DA DG DC SEQRES 1 D 7 DG DT DC DG DG DA DC HET CL A 701 1 HET CL A 702 1 HET NA A 703 1 HET EDO A 704 4 HET AMP D 101 29 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM AMP ADENOSINE MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 CL 2(CL 1-) FORMUL 7 NA NA 1+ FORMUL 8 EDO C2 H6 O2 FORMUL 9 AMP C10 H14 N5 O7 P FORMUL 10 HOH *112(H2 O) HELIX 1 AA1 THR A 9 HIS A 13 5 5 HELIX 2 AA2 PRO A 15 SER A 29 1 15 HELIX 3 AA3 GLY A 31 LYS A 55 1 25 HELIX 4 AA4 PHE A 64 LEU A 72 1 9 HELIX 5 AA5 PRO A 73 GLU A 76 5 4 HELIX 6 AA6 LYS A 85 LEU A 97 1 13 HELIX 7 AA7 GLY A 103 ASN A 111 1 9 HELIX 8 AA8 ASP A 124 LYS A 134 1 11 HELIX 9 AA9 THR A 144 ALA A 161 1 18 HELIX 10 AB1 ARG A 163 GLN A 177 1 15 HELIX 11 AB2 SER A 179 LYS A 192 1 14 HELIX 12 AB3 SER A 199 HIS A 208 1 10 HELIX 13 AB4 ASP A 210 THR A 219 1 10 HELIX 14 AB5 ASP A 220 LEU A 228 1 9 HELIX 15 AB6 ASP A 255 GLU A 257 5 3 HELIX 16 AB7 HIS A 258 MET A 263 1 6 HELIX 17 AB8 TYR A 298 GLY A 303 1 6 HELIX 18 AB9 LEU A 311 HIS A 316 1 6 HELIX 19 AC1 THR A 381 PHE A 393 1 13 HELIX 20 AC2 THR A 410 LYS A 424 1 15 HELIX 21 AC3 LYS A 451 VAL A 455 5 5 HELIX 22 AC4 LYS A 473 GLY A 477 5 5 HELIX 23 AC5 THR A 511 LEU A 522 1 12 HELIX 24 AC6 ALA A 523 TRP A 526 5 4 HELIX 25 AC7 GLU A 550 SER A 554 5 5 HELIX 26 AC8 GLU A 589 CYS A 593 5 5 HELIX 27 AC9 THR A 595 ALA A 606 1 12 SHEET 1 AA1 5 LEU A 250 ILE A 253 0 SHEET 2 AA1 5 ARG A 443 ILE A 450 1 O LYS A 449 N ALA A 252 SHEET 3 AA1 5 ILE A 429 LYS A 432 -1 N VAL A 431 O LEU A 448 SHEET 4 AA1 5 PHE A 268 THR A 272 -1 N GLU A 271 O MET A 430 SHEET 5 AA1 5 THR A 406 ALA A 408 -1 O ALA A 408 N PHE A 268 SHEET 1 AA2 5 VAL A 287 PHE A 291 0 SHEET 2 AA2 5 GLU A 277 ASP A 284 -1 N HIS A 282 O LYS A 289 SHEET 3 AA2 5 ILE A 325 ASN A 336 -1 O MET A 332 N GLU A 277 SHEET 4 AA2 5 GLN A 361 VAL A 372 -1 O CYS A 363 N MET A 333 SHEET 5 AA2 5 LYS A 375 LYS A 376 -1 O LYS A 375 N VAL A 372 SHEET 1 AA3 4 THR A 341 MET A 343 0 SHEET 2 AA3 4 ILE A 325 ASN A 336 -1 N ASN A 336 O THR A 341 SHEET 3 AA3 4 GLN A 361 VAL A 372 -1 O CYS A 363 N MET A 333 SHEET 4 AA3 4 ILE A 400 ILE A 402 1 O GLU A 401 N VAL A 366 SHEET 1 AA4 6 LYS A 527 PRO A 528 0 SHEET 2 AA4 6 VAL A 547 TYR A 548 -1 O TYR A 548 N LYS A 527 SHEET 3 AA4 6 LEU A 462 TRP A 471 -1 N GLY A 469 O VAL A 547 SHEET 4 AA4 6 MET A 480 ALA A 488 -1 O LEU A 484 N VAL A 467 SHEET 5 AA4 6 PHE A 500 VAL A 506 -1 O LEU A 503 N CYS A 485 SHEET 6 AA4 6 ILE A 538 LEU A 539 1 O LEU A 539 N PHE A 500 SHEET 1 AA5 5 LYS A 527 PRO A 528 0 SHEET 2 AA5 5 VAL A 547 TYR A 548 -1 O TYR A 548 N LYS A 527 SHEET 3 AA5 5 LEU A 462 TRP A 471 -1 N GLY A 469 O VAL A 547 SHEET 4 AA5 5 ILE A 556 LYS A 560 -1 O ILE A 559 N LEU A 462 SHEET 5 AA5 5 ARG A 580 ARG A 585 -1 O GLU A 582 N GLN A 558 SHEET 1 AA6 2 GLU A 563 PRO A 566 0 SHEET 2 AA6 2 CYS A 574 ARG A 577 -1 O THR A 575 N VAL A 565 LINK P A DG D 2 O3PAAMP D 101 1555 1555 1.60 LINK P B DG D 2 O3PBAMP D 101 1555 1555 1.60 LINK O GLY A 509 NA NA A 703 1555 1555 2.42 LINK NA NA A 703 O HOH A 801 1555 1555 2.43 LINK NA NA A 703 O HOH A 808 1555 1555 2.43 LINK NA NA A 703 O HOH A 864 1555 1555 2.53 LINK NA NA A 703 OP1 DG D 5 1555 1555 2.43 SITE 1 AC1 2 VAL A 206 ASN A 209 SITE 1 AC2 3 TYR A 298 ASP A 300 GLN A 301 SITE 1 AC3 6 GLY A 509 ILE A 581 HOH A 801 HOH A 808 SITE 2 AC3 6 HOH A 864 DG D 5 SITE 1 AC4 6 ARG A 383 GLU A 514 ASP A 517 LEU A 518 SITE 2 AC4 6 ASP A 586 HOH A 855 SITE 1 AC5 13 GLU A 271 THR A 272 LYS A 273 LEU A 274 SITE 2 AC5 13 ARG A 278 GLU A 331 PHE A 367 MET A 430 SITE 3 AC5 13 LYS A 432 LYS A 449 LYS A 451 DG D 2 SITE 4 AC5 13 HOH P 103 CRYST1 72.657 102.747 110.131 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 0.013763 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009080 0.00000