HEADER LIGASE/DNA 17-DEC-23 8VDT TITLE DNA LIGASE 1 WITH NICK DNA 3'RA:T COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 261-918; COMPND 5 SYNONYM: DNA LIGASE I,POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP] 1; COMPND 6 EC: 6.5.1.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*A)- COMPND 10 D(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(*GP*TP*CP*CP*GP*AP*CP*TP*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 LIGASE, DNA LIGASE 1, LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.KANALELAMPARITHI,M.GULKIS,M.CAGLAYAN REVDAT 1 22-MAY-24 8VDT 0 JRNL AUTH K.E.BALU,M.GULKIS,D.ALMOHDAR,M.CAGLAYAN JRNL TITL STRUCTURES OF LIG1 PROVIDE A MECHANISTIC BASIS FOR JRNL TITL 2 UNDERSTANDING A LACK OF SUGAR DISCRIMINATION AGAINST A JRNL TITL 3 RIBONUCLEOTIDE AT THE 3'-END OF NICK DNA. JRNL REF J.BIOL.CHEM. V. 300 07216 2024 JRNL REFN ESSN 1083-351X JRNL PMID 38522520 JRNL DOI 10.1016/J.JBC.2024.107216 REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 23201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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 24.8300 - 6.6700 0.96 1621 147 0.1592 0.1755 REMARK 3 2 6.6700 - 5.3100 0.98 1552 153 0.2052 0.2652 REMARK 3 3 5.3100 - 4.6500 0.97 1530 142 0.1687 0.2065 REMARK 3 4 4.6500 - 4.2200 0.98 1538 148 0.1701 0.2259 REMARK 3 5 4.2200 - 3.9200 0.96 1501 142 0.1913 0.2340 REMARK 3 6 3.9200 - 3.6900 0.97 1513 137 0.2210 0.2852 REMARK 3 7 3.6900 - 3.5100 0.99 1533 142 0.2158 0.2826 REMARK 3 8 3.5100 - 3.3500 0.98 1487 160 0.2308 0.2871 REMARK 3 9 3.3500 - 3.2300 0.96 1490 126 0.2491 0.3734 REMARK 3 10 3.2300 - 3.1100 0.98 1497 142 0.2473 0.3158 REMARK 3 11 3.1100 - 3.0200 0.99 1543 134 0.2632 0.3172 REMARK 3 12 3.0200 - 2.9300 0.99 1484 148 0.2899 0.3073 REMARK 3 13 2.9300 - 2.8500 0.99 1537 142 0.3485 0.4418 REMARK 3 14 2.8500 - 2.7800 0.92 1379 133 0.3912 0.4136 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) : 0.455 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.66 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 5450 REMARK 3 ANGLE : 0.582 7576 REMARK 3 CHIRALITY : 0.037 868 REMARK 3 PLANARITY : 0.006 868 REMARK 3 DIHEDRAL : 18.126 1031 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): 5.5359 13.2620 30.7958 REMARK 3 T TENSOR REMARK 3 T11: 0.7625 T22: 0.3301 REMARK 3 T33: 0.6123 T12: -0.1397 REMARK 3 T13: 0.0260 T23: -0.0411 REMARK 3 L TENSOR REMARK 3 L11: 1.8878 L22: 2.0490 REMARK 3 L33: 2.8790 L12: -0.0329 REMARK 3 L13: 0.2531 L23: -0.2243 REMARK 3 S TENSOR REMARK 3 S11: -0.2494 S12: 0.1748 S13: 0.0678 REMARK 3 S21: 0.0021 S22: 0.2915 S23: -0.1164 REMARK 3 S31: -0.1689 S32: 0.2270 S33: -0.0602 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 8VDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23397 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 REMARK 200 RESOLUTION RANGE LOW (A) : 24.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER 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: 100MM MES, PH 6.4, 100MM LITHIUM REMARK 280 ACETATE, 12 W/VPEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.5K 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 32.08500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.50100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.67100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.50100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.08500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.67100 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: 6610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 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 PHE A 558 REMARK 465 GLU A 559 REMARK 465 SER A 739 REMARK 465 HIS A 740 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 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 LEU A 261 CG CD1 CD2 REMARK 470 LYS A 270 CE NZ REMARK 470 ASN A 271 OD1 ND2 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 CD OE1 NE2 REMARK 470 LYS A 286 CD CE NZ REMARK 470 LYS A 298 NZ REMARK 470 GLU A 310 OE1 OE2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 ALA A 359 CB REMARK 470 ALA A 361 CB REMARK 470 ARG A 364 CZ NH1 NH2 REMARK 470 GLN A 365 CD OE1 NE2 REMARK 470 LEU A 366 CD1 CD2 REMARK 470 GLU A 367 CB CG CD OE1 OE2 REMARK 470 VAL A 369 CG1 CG2 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 CE NZ REMARK 470 LEU A 381 CG CD1 CD2 REMARK 470 VAL A 382 CG1 CG2 REMARK 470 ASN A 385 CG OD1 ND2 REMARK 470 MET A 393 CG SD CE REMARK 470 LYS A 407 NZ REMARK 470 ASP A 410 OD1 OD2 REMARK 470 LYS A 428 CD CE NZ REMARK 470 ARG A 435 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 475 CB 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 CG CD CE NZ REMARK 470 GLU A 497 CG CD OE1 OE2 REMARK 470 GLU A 498 CG CD OE1 OE2 REMARK 470 ILE A 502 CD1 REMARK 470 GLU A 509 CG CD OE1 OE2 REMARK 470 GLU A 526 CG CD OE1 OE2 REMARK 470 ARG A 527 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 LYS A 533 CB CG CD CE NZ REMARK 470 LEU A 534 CG CD1 CD2 REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 553 CB CG CD OE1 OE2 REMARK 470 VAL A 554 CG1 CG2 REMARK 470 LEU A 555 CD1 CD2 REMARK 470 LYS A 556 CB CG CD CE NZ REMARK 470 GLU A 560 CG CD OE1 OE2 REMARK 470 GLU A 566 CG CD OE1 OE2 REMARK 470 GLU A 580 CG CD OE1 OE2 REMARK 470 GLU A 583 CG CD OE1 OE2 REMARK 470 LYS A 585 CD CE NZ REMARK 470 ILE A 602 CG1 CG2 CD1 REMARK 470 ARG A 604 CB CG CD NE CZ NH1 NH2 REMARK 470 ILE A 605 CB CG1 CG2 CD1 REMARK 470 LYS A 607 CB CG CD CE NZ REMARK 470 LYS A 609 CD CE NZ REMARK 470 LEU A 610 CD1 CD2 REMARK 470 VAL A 613 CG1 CG2 REMARK 470 ARG A 627 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 628 CB CG CD OE1 OE2 REMARK 470 LYS A 629 CB CG CD CE NZ REMARK 470 LYS A 630 CB CG CD CE NZ REMARK 470 GLN A 631 CD OE1 NE2 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 GLU A 650 CG CD OE1 OE2 REMARK 470 ILE A 651 CD1 REMARK 470 GLN A 652 CG CD OE1 NE2 REMARK 470 LEU A 662 CD1 CD2 REMARK 470 ARG A 672 CD NE CZ NH1 NH2 REMARK 470 SER A 676 CB 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 CB CG CD OE1 NE2 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 VAL A 694 CG1 CG2 REMARK 470 ALA A 696 CB REMARK 470 SER A 698 OG REMARK 470 LEU A 699 CG CD1 CD2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 ILE A 704 CG1 CG2 CD1 REMARK 470 GLU A 705 CB CG CD OE1 OE2 REMARK 470 GLN A 706 CB CG CD OE1 NE2 REMARK 470 ILE A 707 CG1 CG2 CD1 REMARK 470 GLU A 712 CD OE1 OE2 REMARK 470 LYS A 716 CG CD CE NZ REMARK 470 GLU A 720 CG CD OE1 OE2 REMARK 470 LEU A 722 CG CD1 CD2 REMARK 470 VAL A 724 CG1 CG2 REMARK 470 VAL A 729 CG1 CG2 REMARK 470 GLU A 734 CB 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 ASN A 741 CG OD1 ND2 REMARK 470 LEU A 743 CD1 CD2 REMARK 470 LYS A 744 CG CD CE NZ REMARK 470 LEU A 745 CD1 CD2 REMARK 470 LEU A 750 CG CD1 CD2 REMARK 470 VAL A 753 CB CG1 CG2 REMARK 470 VAL A 761 CG1 CG2 REMARK 470 ARG A 768 CZ NH1 NH2 REMARK 470 GLU A 785 CG CD OE1 OE2 REMARK 470 GLU A 788 CG CD OE1 OE2 REMARK 470 GLU A 789 CG CD OE1 OE2 REMARK 470 GLU A 806 CG CD OE1 OE2 REMARK 470 GLU A 807 OE1 OE2 REMARK 470 LYS A 813 NZ REMARK 470 ILE A 831 CD1 REMARK 470 ILE A 854 CD1 REMARK 470 ARG A 859 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 866 CG CD CE NZ REMARK 470 LYS A 882 CD CE NZ REMARK 470 GLU A 885 CG CD OE1 OE2 REMARK 470 GLN A 886 CG CD OE1 NE2 REMARK 470 CYS A 895 SG REMARK 470 ARG A 898 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 899 CG CD CE NZ REMARK 470 ILE A 903 CD1 REMARK 470 GLN A 904 CG CD OE1 NE2 REMARK 470 GLN A 906 CG CD OE1 NE2 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 -72.94 -76.96 REMARK 500 HIS A 436 -105.44 59.48 REMARK 500 ALA A 455 -148.81 -140.21 REMARK 500 LYS A 556 -26.20 -140.37 REMARK 500 ALA A 561 149.19 66.91 REMARK 500 LYS A 630 49.32 70.26 REMARK 500 ARG A 643 -140.82 -113.13 REMARK 500 LYS A 644 -108.19 57.13 REMARK 500 GLU A 650 36.86 -97.50 REMARK 500 PHE A 660 12.14 -140.05 REMARK 500 LEU A 665 95.71 -163.38 REMARK 500 ASN A 666 74.84 54.11 REMARK 500 THR A 689 106.28 -160.93 REMARK 500 THR A 697 101.10 -56.12 REMARK 500 LYS A 702 -12.96 -155.97 REMARK 500 SER A 718 73.51 48.76 REMARK 500 ASP A 728 -46.12 -144.29 REMARK 500 LYS A 746 -127.81 -118.07 REMARK 500 ILE A 793 -37.58 -134.88 REMARK 500 HIS A 808 -166.33 -72.22 REMARK 500 HIS A 809 -47.59 60.59 REMARK 500 ASP A 827 -129.45 56.87 REMARK 500 SER A 839 -38.68 -148.94 REMARK 500 ALA A 847 -78.27 -75.17 REMARK 500 ILE A 854 -39.05 -135.19 REMARK 500 VAL A 862 -67.07 -128.50 REMARK 500 GLN A 886 52.11 -101.50 REMARK 500 GLN A 904 20.31 -78.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VDT A 261 918 UNP P18858 DNLI1_HUMAN 261 918 DBREF 8VDT B 1 18 PDB 8VDT 8VDT 1 18 DBREF 8VDT C 1 18 PDB 8VDT 8VDT 1 18 SEQADV 8VDT ALA A 346 UNP P18858 GLU 346 CONFLICT SEQADV 8VDT ALA A 592 UNP P18858 GLU 592 CONFLICT SEQRES 1 A 658 LEU ASP PRO SER GLY TYR ASN PRO ALA LYS ASN ASN TYR SEQRES 2 A 658 HIS PRO VAL GLU ASP ALA CYS TRP LYS PRO GLY GLN LYS SEQRES 3 A 658 VAL PRO TYR LEU ALA VAL ALA ARG THR PHE GLU LYS ILE SEQRES 4 A 658 GLU GLU VAL SER ALA ARG LEU ARG MET VAL GLU THR LEU SEQRES 5 A 658 SER ASN LEU LEU ARG SER VAL VAL ALA LEU SER PRO PRO SEQRES 6 A 658 ASP LEU LEU PRO VAL LEU TYR LEU SER LEU ASN HIS LEU SEQRES 7 A 658 GLY PRO PRO GLN GLN GLY LEU ALA LEU GLY VAL GLY ASP SEQRES 8 A 658 GLY VAL LEU LEU LYS ALA VAL ALA GLN ALA THR GLY ARG SEQRES 9 A 658 GLN LEU GLU SER VAL ARG ALA GLU ALA ALA GLU LYS GLY SEQRES 10 A 658 ASP VAL GLY LEU VAL ALA GLU ASN SER ARG SER THR GLN SEQRES 11 A 658 ARG LEU MET LEU PRO PRO PRO PRO LEU THR ALA SER GLY SEQRES 12 A 658 VAL PHE SER LYS PHE ARG ASP ILE ALA ARG LEU THR GLY SEQRES 13 A 658 SER ALA SER THR ALA LYS LYS ILE ASP ILE ILE LYS GLY SEQRES 14 A 658 LEU PHE VAL ALA CYS ARG HIS SER GLU ALA ARG PHE ILE SEQRES 15 A 658 ALA ARG SER LEU SER GLY ARG LEU ARG LEU GLY LEU ALA SEQRES 16 A 658 GLU GLN SER VAL LEU ALA ALA LEU SER GLN ALA VAL SER SEQRES 17 A 658 LEU THR PRO PRO GLY GLN GLU PHE PRO PRO ALA MET VAL SEQRES 18 A 658 ASP ALA GLY LYS GLY LYS THR ALA GLU ALA ARG LYS THR SEQRES 19 A 658 TRP LEU GLU GLU GLN GLY MET ILE LEU LYS GLN THR PHE SEQRES 20 A 658 CYS GLU VAL PRO ASP LEU ASP ARG ILE ILE PRO VAL LEU SEQRES 21 A 658 LEU GLU HIS GLY LEU GLU ARG LEU PRO GLU HIS CYS LYS SEQRES 22 A 658 LEU SER PRO GLY ILE PRO LEU LYS PRO MET LEU ALA HIS SEQRES 23 A 658 PRO THR ARG GLY ILE SER GLU VAL LEU LYS ARG PHE GLU SEQRES 24 A 658 GLU ALA ALA PHE THR CYS GLU TYR LYS TYR ASP GLY GLN SEQRES 25 A 658 ARG ALA GLN ILE HIS ALA LEU GLU GLY GLY GLU VAL LYS SEQRES 26 A 658 ILE PHE SER ARG ASN GLN ALA ASP ASN THR GLY LYS TYR SEQRES 27 A 658 PRO ASP ILE ILE SER ARG ILE PRO LYS ILE LYS LEU PRO SEQRES 28 A 658 SER VAL THR SER PHE ILE LEU ASP THR GLU ALA VAL ALA SEQRES 29 A 658 TRP ASP ARG GLU LYS LYS GLN ILE GLN PRO PHE GLN VAL SEQRES 30 A 658 LEU THR THR ARG LYS ARG LYS GLU VAL ASP ALA SER GLU SEQRES 31 A 658 ILE GLN VAL GLN VAL CYS LEU TYR ALA PHE ASP LEU ILE SEQRES 32 A 658 TYR LEU ASN GLY GLU SER LEU VAL ARG GLU PRO LEU SER SEQRES 33 A 658 ARG ARG ARG GLN LEU LEU ARG GLU ASN PHE VAL GLU THR SEQRES 34 A 658 GLU GLY GLU PHE VAL PHE ALA THR SER LEU ASP THR LYS SEQRES 35 A 658 ASP ILE GLU GLN ILE ALA GLU PHE LEU GLU GLN SER VAL SEQRES 36 A 658 LYS ASP SER CYS GLU GLY LEU MET VAL LYS THR LEU ASP SEQRES 37 A 658 VAL ASP ALA THR TYR GLU ILE ALA LYS ARG SER HIS ASN SEQRES 38 A 658 TRP LEU LYS LEU LYS LYS ASP TYR LEU ASP GLY VAL GLY SEQRES 39 A 658 ASP THR LEU ASP LEU VAL VAL ILE GLY ALA TYR LEU GLY SEQRES 40 A 658 ARG GLY LYS ARG ALA GLY ARG TYR GLY GLY PHE LEU LEU SEQRES 41 A 658 ALA SER TYR ASP GLU ASP SER GLU GLU LEU GLN ALA ILE SEQRES 42 A 658 CYS LYS LEU GLY THR GLY PHE SER ASP GLU GLU LEU GLU SEQRES 43 A 658 GLU HIS HIS GLN SER LEU LYS ALA LEU VAL LEU PRO SER SEQRES 44 A 658 PRO ARG PRO TYR VAL ARG ILE ASP GLY ALA VAL ILE PRO SEQRES 45 A 658 ASP HIS TRP LEU ASP PRO SER ALA VAL TRP GLU VAL LYS SEQRES 46 A 658 CYS ALA ASP LEU SER LEU SER PRO ILE TYR PRO ALA ALA SEQRES 47 A 658 ARG GLY LEU VAL ASP SER ASP LYS GLY ILE SER LEU ARG SEQRES 48 A 658 PHE PRO ARG PHE ILE ARG VAL ARG GLU ASP LYS GLN PRO SEQRES 49 A 658 GLU GLN ALA THR THR SER ALA GLN VAL ALA CYS LEU TYR SEQRES 50 A 658 ARG LYS GLN SER GLN ILE GLN ASN GLN GLN GLY GLU ASP SEQRES 51 A 658 SER GLY SER ASP PRO GLU ASP THR SEQRES 1 B 18 DG DC DT DG DA DT DG DC DG DT DA DG DT SEQRES 2 B 18 DC DG DG DA DC SEQRES 1 C 18 DG DT DC DC DG DA DC DT DA DC DG DC DA SEQRES 2 C 18 DT DC DA DG DC HET PO4 B 101 5 HETNAM PO4 PHOSPHATE ION FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *25(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 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 THR A 362 1 13 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 ARG A 413 1 14 HELIX 10 AB1 ALA A 418 VAL A 432 1 15 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 LEU A 555 1 6 HELIX 16 AB7 ASN A 594 LYS A 597 5 4 HELIX 17 AB8 TYR A 598 ARG A 604 1 7 HELIX 18 AB9 ILE A 605 ILE A 608 5 4 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 ASN A 685 1 12 HELIX 22 AC4 ASP A 703 ASP A 717 1 15 HELIX 23 AC5 ARG A 768 ALA A 772 5 5 HELIX 24 AC6 SER A 801 SER A 811 1 11 HELIX 25 AC7 LEU A 812 ALA A 814 5 3 HELIX 26 AC8 GLN A 883 ALA A 887 5 5 HELIX 27 AC9 THR A 889 LYS A 899 1 11 SHEET 1 AA1 3 PHE A 563 LYS A 568 0 SHEET 2 AA1 3 GLY A 721 THR A 726 -1 O MET A 723 N GLU A 566 SHEET 3 AA1 3 LEU A 743 LEU A 745 -1 O LEU A 745 N LEU A 722 SHEET 1 AA2 5 VAL A 584 SER A 588 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 ALA A 624 -1 O ALA A 622 N GLN A 572 SHEET 4 AA2 5 LEU A 662 LEU A 665 -1 O ILE A 663 N ILE A 617 SHEET 5 AA2 5 GLU A 668 SER A 669 -1 O GLU A 668 N LEU A 665 SHEET 1 AA3 5 VAL A 584 SER A 588 0 SHEET 2 AA3 5 GLN A 572 ALA A 578 -1 N HIS A 577 O LYS A 585 SHEET 3 AA3 5 PHE A 616 ALA A 624 -1 O ALA A 622 N GLN A 572 SHEET 4 AA3 5 VAL A 655 ALA A 659 -1 O CYS A 656 N VAL A 623 SHEET 5 AA3 5 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 ASP A 755 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 GLN A 791 N SER A 782 SHEET 6 AA4 6 VAL A 824 ARG A 825 1 O ARG A 825 N ALA A 792 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 ASP A 755 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA5 5 VAL A 841 CYS A 846 -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 LEU A 849 SER A 852 0 SHEET 2 AA6 2 GLY A 867 LEU A 870 -1 O SER A 869 N SER A 850 CISPEP 1 PHE A 476 PRO A 477 0 -6.71 CRYST1 64.170 115.342 125.002 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 0.015584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008000 0.00000