HEADER LIGASE/DNA 22-NOV-21 7SXE TITLE CRYSTAL STRUCTURE OF LIGASE I WITH NICK DUPLEXES CONTAINING COGNATE TITLE 2 G: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 CHAIN 1; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA CHAIN 2; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA CHAIN 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: 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 LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.TANG,M.GULKIS,R.MCKENNA,M.CAGLAYAN REVDAT 4 18-OCT-23 7SXE 1 REMARK REVDAT 3 21-SEP-22 7SXE 1 REMARK REVDAT 2 20-JUL-22 7SXE 1 JRNL REVDAT 1 13-JUL-22 7SXE 0 JRNL AUTH Q.TANG,M.GULKIS,R.MCKENNA,M.CAGLAYAN JRNL TITL STRUCTURES OF LIG1 THAT ENGAGE WITH MUTAGENIC MISMATCHES JRNL TITL 2 INSERTED BY POL BETA IN BASE EXCISION REPAIR. JRNL REF NAT COMMUN V. 13 3860 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35790757 JRNL DOI 10.1038/S41467-022-31585-W REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19239 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 996 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 19.9700 - 5.7000 1.00 2765 142 0.1674 0.2146 REMARK 3 2 5.7000 - 4.5400 0.99 2603 161 0.1798 0.2139 REMARK 3 3 4.5400 - 3.9700 1.00 2599 155 0.1909 0.2082 REMARK 3 4 3.9700 - 3.6100 1.00 2606 137 0.2299 0.3007 REMARK 3 5 3.6100 - 3.3500 0.99 2541 155 0.2478 0.2808 REMARK 3 6 3.3500 - 3.1600 0.98 2560 107 0.2706 0.3687 REMARK 3 7 3.1600 - 3.0000 1.00 2569 139 0.3182 0.3575 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.91 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7SXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000260252. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-21 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 : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19288 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> 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: PDB ENTRY 7SUM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, PH 6.6, 100 MM LITHIUM REMARK 280 ACETATE, 20% W/V PEG3350, VAPOR DIFFUSION, HANGING 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 32.12700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.81600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.99900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.81600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.12700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.99900 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: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 388 REMARK 465 THR A 389 REMARK 465 GLN A 390 REMARK 465 ARG A 391 REMARK 465 LEU A 392 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 ASN A 271 CG OD1 ND2 REMARK 470 ASN A 272 CG OD1 ND2 REMARK 470 LYS A 282 CG CD CE NZ REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 ARG A 364 CG CD NE CZ NH1 NH2 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 CG CD CE NZ REMARK 470 ASN A 385 CG OD1 ND2 REMARK 470 ARG A 387 CG CD NE CZ NH1 NH2 REMARK 470 MET A 393 CG SD CE REMARK 470 LYS A 428 CG CD CE NZ REMARK 470 ARG A 435 CG CD NE 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 GLU A 497 CG CD OE1 OE2 REMARK 470 GLU A 509 CG CD OE1 OE2 REMARK 470 GLU A 526 CG CD OE1 OE2 REMARK 470 ARG A 527 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 530 CG CD OE1 OE2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 ARG A 549 CG CD NE CZ NH1 NH2 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 GLU A 580 CG CD OE1 OE2 REMARK 470 LYS A 585 CG CD CE NZ REMARK 470 LYS A 607 CG CD CE NZ REMARK 470 LYS A 609 CG CD CE NZ REMARK 470 GLU A 628 CG CD OE1 OE2 REMARK 470 LYS A 629 CG CD CE NZ REMARK 470 LYS A 630 CG CD CE NZ REMARK 470 GLN A 631 CG 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 ASP A 647 CG OD1 OD2 REMARK 470 GLU A 650 CG CD OE1 OE2 REMARK 470 ARG A 672 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 677 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 680 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 LEU A 699 CG CD1 CD2 REMARK 470 LYS A 702 CG CD CE NZ REMARK 470 GLU A 705 CG CD OE1 OE2 REMARK 470 GLN A 706 CG CD OE1 NE2 REMARK 470 GLU A 709 CG CD OE1 OE2 REMARK 470 GLU A 712 CG CD OE1 OE2 REMARK 470 LYS A 716 CG CD CE NZ REMARK 470 LYS A 737 CG CD CE NZ REMARK 470 ARG A 738 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 744 CG CD CE NZ REMARK 470 LYS A 746 CG CD CE NZ REMARK 470 LYS A 747 CG CD CE NZ REMARK 470 ASP A 751 CG OD1 OD2 REMARK 470 TYR A 783 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 789 CG CD OE1 OE2 REMARK 470 LYS A 813 CG CD CE NZ REMARK 470 LYS A 845 CG CD CE NZ REMARK 470 ARG A 859 CG CD NE CZ NH1 NH2 REMARK 470 SER A 869 OG REMARK 470 ARG A 877 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 879 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 882 CG CD CE NZ REMARK 470 GLU A 885 CG CD OE1 OE2 REMARK 470 LYS A 899 CG CD CE NZ REMARK 470 GLN A 902 CG CD OE1 NE2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 754 REMARK 475 LYS A 813 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 270 CG CD CE NZ REMARK 480 GLN A 365 CG CD OE1 NE2 REMARK 480 LEU A 366 CG CD1 CD2 REMARK 480 GLU A 367 CB CG OE1 OE2 REMARK 480 GLU A 372 CG REMARK 480 SER A 386 OG REMARK 480 ASP A 751 N CA C O REMARK 480 ARG A 825 CZ NH1 NH2 REMARK 480 GLN A 886 CD OE1 NE2 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 DG C 1 P DG C 1 OP3 -0.128 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 ASP A 262 102.27 -52.65 REMARK 500 SER A 264 6.00 -65.39 REMARK 500 SER A 264 4.80 -64.26 REMARK 500 ALA A 279 173.86 -59.87 REMARK 500 THR A 362 -33.96 -144.92 REMARK 500 ILE A 424 -19.85 -48.89 REMARK 500 HIS A 436 -112.38 57.31 REMARK 500 ARG A 440 -52.13 -29.18 REMARK 500 ARG A 451 62.38 32.77 REMARK 500 ALA A 455 -145.77 -134.79 REMARK 500 ASP A 570 68.42 -100.73 REMARK 500 GLU A 580 105.98 -45.13 REMARK 500 ARG A 604 7.81 -62.69 REMARK 500 LYS A 607 4.36 -64.24 REMARK 500 ARG A 643 -150.46 -93.13 REMARK 500 LYS A 644 -121.55 40.42 REMARK 500 GLU A 650 -7.50 -54.79 REMARK 500 GLN A 652 -37.91 -139.38 REMARK 500 GLU A 692 -58.97 -139.51 REMARK 500 LEU A 699 94.19 -161.12 REMARK 500 THR A 701 -179.96 -170.38 REMARK 500 LYS A 702 13.35 -142.54 REMARK 500 SER A 718 64.18 73.25 REMARK 500 ASP A 728 -47.04 -138.54 REMARK 500 ASP A 730 59.13 31.67 REMARK 500 LYS A 737 -71.60 -69.58 REMARK 500 HIS A 740 52.45 -103.16 REMARK 500 ASP A 751 109.87 -34.72 REMARK 500 TYR A 783 109.84 -46.96 REMARK 500 HIS A 808 -70.49 -76.13 REMARK 500 GLN A 810 -73.83 -79.67 REMARK 500 LEU A 815 -6.86 -56.90 REMARK 500 ASP A 827 -130.70 64.53 REMARK 500 PRO A 838 95.13 -61.18 REMARK 500 SER A 839 -55.64 -124.80 REMARK 500 LEU A 851 98.95 -68.82 REMARK 500 ILE A 854 -2.65 -143.44 REMARK 500 ARG A 879 72.27 -113.05 REMARK 500 GLN A 900 67.17 -150.51 REMARK 500 SER A 901 61.00 38.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AMP A 1001 DBREF 7SXE A 261 918 UNP P18858 DNLI1_HUMAN 261 918 DBREF 7SXE B 3 13 PDB 7SXE 7SXE 3 13 DBREF 7SXE C 1 7 PDB 7SXE 7SXE 1 7 DBREF 7SXE D 9 26 PDB 7SXE 7SXE 9 26 SEQADV 7SXE ALA A 346 UNP P18858 GLU 346 CONFLICT SEQADV 7SXE ALA A 592 UNP P18858 GLU 592 CONFLICT SEQADV 7SXE ALA A 919 UNP P18858 EXPRESSION TAG SEQADV 7SXE ALA A 920 UNP P18858 EXPRESSION TAG SEQADV 7SXE ALA A 921 UNP P18858 EXPRESSION TAG SEQADV 7SXE LEU A 922 UNP P18858 EXPRESSION TAG SEQADV 7SXE GLU A 923 UNP P18858 EXPRESSION TAG SEQADV 7SXE HIS A 924 UNP P18858 EXPRESSION TAG SEQADV 7SXE HIS A 925 UNP P18858 EXPRESSION TAG SEQADV 7SXE HIS A 926 UNP P18858 EXPRESSION TAG SEQADV 7SXE HIS A 927 UNP P18858 EXPRESSION TAG SEQADV 7SXE HIS A 928 UNP P18858 EXPRESSION TAG SEQADV 7SXE HIS A 929 UNP P18858 EXPRESSION TAG SEQRES 1 A 669 LEU ASP PRO SER GLY TYR ASN PRO ALA LYS ASN ASN TYR SEQRES 2 A 669 HIS PRO VAL GLU ASP ALA CYS TRP LYS PRO GLY GLN LYS SEQRES 3 A 669 VAL PRO TYR LEU ALA VAL ALA ARG THR PHE GLU LYS ILE SEQRES 4 A 669 GLU GLU VAL SER ALA ARG LEU ARG MET VAL GLU THR LEU SEQRES 5 A 669 SER ASN LEU LEU ARG SER VAL VAL ALA LEU SER PRO PRO SEQRES 6 A 669 ASP LEU LEU PRO VAL LEU TYR LEU SER LEU ASN HIS LEU SEQRES 7 A 669 GLY PRO PRO GLN GLN GLY LEU ALA LEU GLY VAL GLY ASP SEQRES 8 A 669 GLY VAL LEU LEU LYS ALA VAL ALA GLN ALA THR GLY ARG SEQRES 9 A 669 GLN LEU GLU SER VAL ARG ALA GLU ALA ALA GLU LYS GLY SEQRES 10 A 669 ASP VAL GLY LEU VAL ALA GLU ASN SER ARG SER THR GLN SEQRES 11 A 669 ARG LEU MET LEU PRO PRO PRO PRO LEU THR ALA SER GLY SEQRES 12 A 669 VAL PHE SER LYS PHE ARG ASP ILE ALA ARG LEU THR GLY SEQRES 13 A 669 SER ALA SER THR ALA LYS LYS ILE ASP ILE ILE LYS GLY SEQRES 14 A 669 LEU PHE VAL ALA CYS ARG HIS SER GLU ALA ARG PHE ILE SEQRES 15 A 669 ALA ARG SER LEU SER GLY ARG LEU ARG LEU GLY LEU ALA SEQRES 16 A 669 GLU GLN SER VAL LEU ALA ALA LEU SER GLN ALA VAL SER SEQRES 17 A 669 LEU THR PRO PRO GLY GLN GLU PHE PRO PRO ALA MET VAL SEQRES 18 A 669 ASP ALA GLY LYS GLY LYS THR ALA GLU ALA ARG LYS THR SEQRES 19 A 669 TRP LEU GLU GLU GLN GLY MET ILE LEU LYS GLN THR PHE SEQRES 20 A 669 CYS GLU VAL PRO ASP LEU ASP ARG ILE ILE PRO VAL LEU SEQRES 21 A 669 LEU GLU HIS GLY LEU GLU ARG LEU PRO GLU HIS CYS LYS SEQRES 22 A 669 LEU SER PRO GLY ILE PRO LEU LYS PRO MET LEU ALA HIS SEQRES 23 A 669 PRO THR ARG GLY ILE SER GLU VAL LEU LYS ARG PHE GLU SEQRES 24 A 669 GLU ALA ALA PHE THR CYS GLU TYR LYS TYR ASP GLY GLN SEQRES 25 A 669 ARG ALA GLN ILE HIS ALA LEU GLU GLY GLY GLU VAL LYS SEQRES 26 A 669 ILE PHE SER ARG ASN GLN ALA ASP ASN THR GLY LYS TYR SEQRES 27 A 669 PRO ASP ILE ILE SER ARG ILE PRO LYS ILE LYS LEU PRO SEQRES 28 A 669 SER VAL THR SER PHE ILE LEU ASP THR GLU ALA VAL ALA SEQRES 29 A 669 TRP ASP ARG GLU LYS LYS GLN ILE GLN PRO PHE GLN VAL SEQRES 30 A 669 LEU THR THR ARG LYS ARG LYS GLU VAL ASP ALA SER GLU SEQRES 31 A 669 ILE GLN VAL GLN VAL CYS LEU TYR ALA PHE ASP LEU ILE SEQRES 32 A 669 TYR LEU ASN GLY GLU SER LEU VAL ARG GLU PRO LEU SER SEQRES 33 A 669 ARG ARG ARG GLN LEU LEU ARG GLU ASN PHE VAL GLU THR SEQRES 34 A 669 GLU GLY GLU PHE VAL PHE ALA THR SER LEU ASP THR LYS SEQRES 35 A 669 ASP ILE GLU GLN ILE ALA GLU PHE LEU GLU GLN SER VAL SEQRES 36 A 669 LYS ASP SER CYS GLU GLY LEU MET VAL LYS THR LEU ASP SEQRES 37 A 669 VAL ASP ALA THR TYR GLU ILE ALA LYS ARG SER HIS ASN SEQRES 38 A 669 TRP LEU LYS LEU LYS LYS ASP TYR LEU ASP GLY VAL GLY SEQRES 39 A 669 ASP THR LEU ASP LEU VAL VAL ILE GLY ALA TYR LEU GLY SEQRES 40 A 669 ARG GLY LYS ARG ALA GLY ARG TYR GLY GLY PHE LEU LEU SEQRES 41 A 669 ALA SER TYR ASP GLU ASP SER GLU GLU LEU GLN ALA ILE SEQRES 42 A 669 CYS LYS LEU GLY THR GLY PHE SER ASP GLU GLU LEU GLU SEQRES 43 A 669 GLU HIS HIS GLN SER LEU LYS ALA LEU VAL LEU PRO SER SEQRES 44 A 669 PRO ARG PRO TYR VAL ARG ILE ASP GLY ALA VAL ILE PRO SEQRES 45 A 669 ASP HIS TRP LEU ASP PRO SER ALA VAL TRP GLU VAL LYS SEQRES 46 A 669 CYS ALA ASP LEU SER LEU SER PRO ILE TYR PRO ALA ALA SEQRES 47 A 669 ARG GLY LEU VAL ASP SER ASP LYS GLY ILE SER LEU ARG SEQRES 48 A 669 PHE PRO ARG PHE ILE ARG VAL ARG GLU ASP LYS GLN PRO SEQRES 49 A 669 GLU GLN ALA THR THR SER ALA GLN VAL ALA CYS LEU TYR SEQRES 50 A 669 ARG LYS GLN SER GLN ILE GLN ASN GLN GLN GLY GLU ASP SEQRES 51 A 669 SER GLY SER ASP PRO GLU ASP THR ALA ALA ALA LEU GLU SEQRES 52 A 669 HIS HIS HIS HIS HIS HIS SEQRES 1 B 11 DG DC DT DG DA DT DG DC DG DT DG SEQRES 1 C 7 DG DT DC DG DG DA DC SEQRES 1 D 18 DG DT DC DC DG DA DC DT DA DC DG DC DA SEQRES 2 D 18 DT DC DA DG DC HET AMP A1001 22 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 HOH *37(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 SER A 386 1 9 HELIX 9 AA9 THR A 400 LEU A 414 1 15 HELIX 10 AB1 ALA A 418 ALA A 433 1 16 HELIX 11 AB2 SER A 437 SER A 447 1 11 HELIX 12 AB3 ALA A 455 THR A 470 1 16 HELIX 13 AB4 THR A 488 VAL A 510 1 23 HELIX 14 AB5 ASP A 512 GLY A 524 1 13 HELIX 15 AB6 ARG A 527 CYS A 532 1 6 HELIX 16 AB7 ILE A 551 PHE A 558 1 8 HELIX 17 AB8 ASN A 594 LYS A 597 5 4 HELIX 18 AB9 TYR A 598 SER A 603 1 6 HELIX 19 AC1 PRO A 634 THR A 639 1 6 HELIX 20 AC2 VAL A 671 GLU A 673 5 3 HELIX 21 AC3 PRO A 674 GLU A 684 1 11 HELIX 22 AC4 ASP A 703 ASP A 717 1 15 HELIX 23 AC5 ASP A 748 LEU A 750 5 3 HELIX 24 AC6 ARG A 768 ALA A 772 5 5 HELIX 25 AC7 SER A 801 LEU A 815 1 15 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 4 ALA A 545 PRO A 547 0 SHEET 2 AA1 4 TRP A 742 LYS A 746 1 O LYS A 744 N HIS A 546 SHEET 3 AA1 4 GLY A 721 THR A 726 -1 N LEU A 722 O LEU A 745 SHEET 4 AA1 4 PHE A 563 TYR A 567 -1 N GLU A 566 O MET A 723 SHEET 1 AA2 4 VAL A 584 SER A 588 0 SHEET 2 AA2 4 GLN A 572 ALA A 578 -1 N GLN A 575 O PHE A 587 SHEET 3 AA2 4 PHE A 616 ASP A 626 -1 O PHE A 616 N ALA A 578 SHEET 4 AA2 4 VAL A 655 LEU A 657 -1 O CYS A 656 N VAL A 623 SHEET 1 AA3 4 GLN A 631 GLN A 633 0 SHEET 2 AA3 4 PHE A 616 ASP A 626 -1 N ASP A 626 O GLN A 631 SHEET 3 AA3 4 LEU A 662 LEU A 665 -1 O ILE A 663 N ILE A 617 SHEET 4 AA3 4 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 THR A 756 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA4 6 TYR A 775 ALA A 781 -1 O ALA A 781 N VAL A 760 SHEET 5 AA4 6 LEU A 790 LEU A 796 -1 O ILE A 793 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 THR A 756 LEU A 766 -1 N ALA A 764 O HIS A 834 SHEET 4 AA5 5 VAL A 841 LYS A 845 -1 O VAL A 844 N LEU A 757 SHEET 5 AA5 5 ARG A 874 VAL A 878 -1 O ARG A 877 N GLU A 843 SHEET 1 AA6 2 ASP A 848 SER A 852 0 SHEET 2 AA6 2 GLY A 867 ARG A 871 -1 O SER A 869 N SER A 850 CISPEP 1 PHE A 476 PRO A 477 0 -3.81 CRYST1 64.254 115.998 125.632 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 0.015563 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007960 0.00000