HEADER LIGASE/DNA 16-DEC-23 8VDN TITLE DNA LIGASE 1 WITH NICK DG:C 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 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DOWNSTREAM OLIGO; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: UPSTREAM OLIGO; COMPND 15 CHAIN: B; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: TEMPLATE OLIGO; 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 LIG1, DNA LIGASE 1, LIGASE, LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.KANALELAMPARITHI,M.GULKIS,M.CAGLAYAN REVDAT 1 22-MAY-24 8VDN 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. 2.39 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 37843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.250 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 39.5200 - 5.7600 0.99 2754 149 0.1669 0.1845 REMARK 3 2 5.7600 - 4.5800 0.99 2613 146 0.1718 0.2246 REMARK 3 3 4.5800 - 4.0000 1.00 2622 142 0.1654 0.1882 REMARK 3 4 4.0000 - 3.6300 1.00 2575 149 0.2140 0.2627 REMARK 3 5 3.6300 - 3.3700 0.99 2579 142 0.2128 0.2298 REMARK 3 6 3.3700 - 3.1700 0.98 2526 142 0.2293 0.2769 REMARK 3 7 3.1700 - 3.0200 1.00 2564 136 0.2740 0.3270 REMARK 3 8 3.0100 - 2.8800 1.00 2553 138 0.2885 0.3115 REMARK 3 9 2.8800 - 2.7700 0.99 2543 152 0.2722 0.2912 REMARK 3 10 2.7700 - 2.6800 1.00 2535 146 0.2644 0.3383 REMARK 3 11 2.6800 - 2.5900 0.99 2544 127 0.2667 0.2991 REMARK 3 12 2.5900 - 2.5200 0.99 2514 148 0.2878 0.3369 REMARK 3 13 2.5200 - 2.4500 0.99 2522 141 0.3399 0.3766 REMARK 3 14 2.4500 - 2.3900 0.94 2412 129 0.4104 0.4821 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) : 0.398 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.068 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 5653 REMARK 3 ANGLE : 0.555 7842 REMARK 3 CHIRALITY : 0.036 898 REMARK 3 PLANARITY : 0.005 896 REMARK 3 DIHEDRAL : 18.574 1042 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): -5.2941 13.6243 -30.9316 REMARK 3 T TENSOR REMARK 3 T11: 0.4880 T22: 0.2947 REMARK 3 T33: 0.5125 T12: 0.0668 REMARK 3 T13: 0.0112 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.8724 L22: 3.0438 REMARK 3 L33: 3.3650 L12: -0.1146 REMARK 3 L13: 0.0092 L23: 0.2681 REMARK 3 S TENSOR REMARK 3 S11: -0.0900 S12: 0.0041 S13: 0.0777 REMARK 3 S21: -0.5478 S22: 0.0991 S23: 0.0878 REMARK 3 S31: -0.2471 S32: -0.1554 S33: -0.0222 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 8VDN 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_1000279921. 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 : NULL 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) : 1.0000 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 : 38037 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 1.100 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 (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, PH 6.4, 100 MM LITHIUM REMARK 280 ACETATE, 12% W/V PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.15K 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 32.48850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.08750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.81550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.08750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.48850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.81550 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: 7580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, 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 PHE A 558 REMARK 465 GLU A 559 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 LYS A 282 CG CD CE NZ REMARK 470 LYS A 286 CD CE NZ REMARK 470 LYS A 298 NZ REMARK 470 GLU A 310 OE1 OE2 REMARK 470 ALA A 359 CB REMARK 470 ALA A 361 CB REMARK 470 ARG A 364 CZ NH1 NH2 REMARK 470 LEU A 366 CD1 CD2 REMARK 470 ARG A 370 CG 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 CB CG CD1 CD2 REMARK 470 ASN A 385 CG OD1 ND2 REMARK 470 MET A 393 CG SD CE REMARK 470 LYS A 407 NZ 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 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 522 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 ARG A 549 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 553 CD OE1 OE2 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 ARG A 604 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 607 CG CD CE NZ REMARK 470 VAL A 613 CG1 CG2 REMARK 470 GLU A 628 CD OE1 OE2 REMARK 470 LYS A 629 CG CD CE NZ REMARK 470 LYS A 630 CB 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 GLU A 668 CG CD OE1 OE2 REMARK 470 ARG A 672 CD NE CZ NH1 NH2 REMARK 470 ARG A 677 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 680 CB CG CD OE1 NE2 REMARK 470 ARG A 683 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 690 CG CD OE1 OE2 REMARK 470 ALA A 696 CB REMARK 470 SER A 698 OG 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 LYS A 716 CG CD CE NZ 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 LEU A 745 CD1 CD2 REMARK 470 VAL A 753 CB CG1 CG2 REMARK 470 ARG A 768 CZ NH1 NH2 REMARK 470 GLU A 785 CG CD OE1 OE2 REMARK 470 GLU A 789 CG CD OE1 OE2 REMARK 470 GLU A 803 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 LYS A 882 CD CE NZ REMARK 470 CYS A 895 SG REMARK 470 LYS A 899 CG CD CE NZ REMARK 470 ILE A 903 CD1 REMARK 470 GLN A 906 CG CD OE1 NE2 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 6 O4' - C1' - N1 ANGL. DEV. = 2.0 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 -100.91 58.79 REMARK 500 ALA A 455 -146.28 -124.63 REMARK 500 ARG A 549 -77.42 -65.32 REMARK 500 TYR A 598 71.67 -119.21 REMARK 500 GLU A 692 -31.29 -135.60 REMARK 500 ASP A 700 70.18 -107.66 REMARK 500 THR A 701 -168.83 -127.66 REMARK 500 LYS A 702 17.18 -144.21 REMARK 500 ASP A 728 -49.40 -140.33 REMARK 500 ARG A 774 -159.53 -137.75 REMARK 500 ASP A 827 -129.30 57.12 REMARK 500 SER A 839 -33.34 -157.25 REMARK 500 ILE A 854 -32.84 -140.21 REMARK 500 ILE A 876 -68.00 -108.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 8VDN A 261 918 UNP P18858 DNLI1_HUMAN 261 918 DBREF 8VDN C 1 7 PDB 8VDN 8VDN 1 7 DBREF 8VDN B 1 11 PDB 8VDN 8VDN 1 11 DBREF 8VDN D 1 18 PDB 8VDN 8VDN 1 18 SEQADV 8VDN ALA A 346 UNP P18858 GLU 346 ENGINEERED MUTATION SEQADV 8VDN ALA A 592 UNP P18858 GLU 592 ENGINEERED MUTATION 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 C 7 DG DT DC DG DG DA DC SEQRES 1 B 11 DG DC DT DG DA DT DG DC DG DT DG 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 AMP C 101 23 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 HOH *38(H2 O) HELIX 1 AA1 PRO A 288 VAL A 302 1 15 HELIX 2 AA2 ALA A 304 SER A 323 1 20 HELIX 3 AA3 ASP A 326 ASN A 336 1 11 HELIX 4 AA4 PRO A 340 GLY A 344 5 5 HELIX 5 AA5 GLY A 350 GLY A 363 1 14 HELIX 6 AA6 GLN A 365 GLY A 377 1 13 HELIX 7 AA7 VAL A 379 ASN A 385 1 7 HELIX 8 AA8 THR A 400 LEU A 414 1 15 HELIX 9 AA9 ALA A 418 VAL A 432 1 15 HELIX 10 AB1 SER A 437 GLY A 448 1 12 HELIX 11 AB2 ALA A 455 THR A 470 1 16 HELIX 12 AB3 THR A 488 VAL A 510 1 23 HELIX 13 AB4 ASP A 512 GLY A 524 1 13 HELIX 14 AB5 ARG A 527 CYS A 532 1 6 HELIX 15 AB6 GLY A 550 LYS A 556 1 7 HELIX 16 AB7 TYR A 598 ARG A 604 1 7 HELIX 17 AB8 ILE A 605 LYS A 609 5 5 HELIX 18 AB9 PRO A 634 THR A 639 1 6 HELIX 19 AC1 PRO A 674 PHE A 686 1 13 HELIX 20 AC2 ASP A 703 ASP A 717 1 15 HELIX 21 AC3 ASP A 748 LEU A 750 5 3 HELIX 22 AC4 ARG A 768 ALA A 772 5 5 HELIX 23 AC5 SER A 801 LEU A 812 1 12 HELIX 24 AC6 GLN A 883 ALA A 887 5 5 HELIX 25 AC7 THR A 889 LYS A 899 1 11 HELIX 26 AC8 GLN A 900 ASN A 905 1 6 SHEET 1 AA1 5 ALA A 545 PRO A 547 0 SHEET 2 AA1 5 TRP A 742 LYS A 746 1 O TRP A 742 N HIS A 546 SHEET 3 AA1 5 GLY A 721 THR A 726 -1 N VAL A 724 O LEU A 743 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 4 VAL A 584 PHE A 587 0 SHEET 2 AA2 4 GLN A 572 ALA A 578 -1 N HIS A 577 O LYS A 585 SHEET 3 AA2 4 PHE A 616 ASP A 626 -1 O PHE A 616 N ALA A 578 SHEET 4 AA2 4 GLN A 631 ILE A 632 -1 O GLN A 631 N ASP A 626 SHEET 1 AA3 5 VAL A 584 PHE A 587 0 SHEET 2 AA3 5 GLN A 572 ALA A 578 -1 N HIS A 577 O LYS A 585 SHEET 3 AA3 5 PHE A 616 ASP A 626 -1 O PHE A 616 N ALA A 578 SHEET 4 AA3 5 VAL A 655 LEU A 665 -1 O CYS A 656 N VAL A 623 SHEET 5 AA3 5 GLU A 668 SER A 669 -1 O GLU A 668 N LEU A 665 SHEET 1 AA4 6 VAL A 816 LEU A 817 0 SHEET 2 AA4 6 HIS A 834 LEU A 836 -1 O TRP A 835 N LEU A 817 SHEET 3 AA4 6 ASP A 755 LEU A 766 -1 N ILE A 762 O LEU A 836 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 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 ASP A 755 LEU A 766 -1 N ILE A 762 O LEU A 836 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 ASP A 848 SER A 852 0 SHEET 2 AA6 2 GLY A 867 ARG A 871 -1 O ARG A 871 N ASP A 848 LINK P DG C 1 O3P AMP C 101 1555 1555 1.56 CISPEP 1 PHE A 476 PRO A 477 0 -2.18 CRYST1 64.977 115.631 126.175 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 0.015390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007926 0.00000