PDB Short entry for 5IIJ HEADER TRANSFERASE/DNA 01-MAR-16 5IIJ TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF DNA TITLE 2 POLYMERASE LAMBDA WITH A TEMPLATING 8-OXO-DG AND AN INCOMING DCTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 5 KAPPA; COMPND 6 EC: 2.7.7.7,4.2.99.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3'); COMPND 18 CHAIN: T; 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: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ REVDAT 3 06-MAR-24 5IIJ 1 JRNL REMARK LINK REVDAT 2 28-SEP-16 5IIJ 1 JRNL REVDAT 1 17-AUG-16 5IIJ 0 JRNL AUTH M.J.BURAK,K.E.GUJA,E.HAMBARDJIEVA,B.DERKUNT,M.GARCIA-DIAZ JRNL TITL A FIDELITY MECHANISM IN DNA POLYMERASE LAMBDA PROMOTES JRNL TITL 2 ERROR-FREE BYPASS OF 8-OXO-DG. JRNL REF EMBO J. V. 35 2045 2016 JRNL REFN ESSN 1460-2075 JRNL PMID 27481934 JRNL DOI 10.15252/EMBJ.201694332 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 52694 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2598 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 41.7183 - 4.5994 0.99 2835 148 0.1752 0.1919 REMARK 3 2 4.5994 - 3.6514 1.00 2703 138 0.1622 0.1835 REMARK 3 3 3.6514 - 3.1900 1.00 2699 136 0.1816 0.2146 REMARK 3 4 3.1900 - 2.8984 1.00 2658 130 0.1993 0.2255 REMARK 3 5 2.8984 - 2.6907 1.00 2635 151 0.2117 0.2213 REMARK 3 6 2.6907 - 2.5321 1.00 2666 119 0.2130 0.2461 REMARK 3 7 2.5321 - 2.4053 1.00 2616 139 0.2135 0.2672 REMARK 3 8 2.4053 - 2.3006 1.00 2623 156 0.2120 0.2470 REMARK 3 9 2.3006 - 2.2121 1.00 2599 140 0.2099 0.2362 REMARK 3 10 2.2121 - 2.1357 1.00 2624 133 0.2025 0.2369 REMARK 3 11 2.1357 - 2.0690 1.00 2641 108 0.2073 0.2410 REMARK 3 12 2.0690 - 2.0098 1.00 2607 138 0.2089 0.2530 REMARK 3 13 2.0098 - 1.9569 1.00 2599 142 0.2126 0.2429 REMARK 3 14 1.9569 - 1.9092 1.00 2577 125 0.2398 0.2871 REMARK 3 15 1.9092 - 1.8658 1.00 2612 151 0.2397 0.2622 REMARK 3 16 1.8658 - 1.8261 1.00 2587 153 0.2345 0.2647 REMARK 3 17 1.8261 - 1.7895 1.00 2594 124 0.2396 0.2567 REMARK 3 18 1.7895 - 1.7558 1.00 2601 130 0.2503 0.2783 REMARK 3 19 1.7558 - 1.7244 1.00 2620 137 0.2597 0.2768 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.350 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 : 0.007 2942 REMARK 3 ANGLE : 1.071 4074 REMARK 3 CHIRALITY : 0.043 450 REMARK 3 PLANARITY : 0.005 450 REMARK 3 DIHEDRAL : 17.483 1084 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 5IIJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-15 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 : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.724 REMARK 200 RESOLUTION RANGE LOW (A) : 70.038 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL 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 (%): 57.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 7.0 AND 1.0 REMARK 280 M SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 27.87450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.03800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.03800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.87450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.42500 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: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T 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 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 465 VAL A 537 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 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 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 259 CD CE NZ REMARK 470 LYS A 265 CD CE NZ REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 LEU A 286 CD1 CD2 REMARK 470 LYS A 287 CE NZ REMARK 470 SER A 295 OG REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 SER A 319 OG REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CD CE NZ REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 449 CG OD1 OD2 REMARK 470 GLN A 453 CD OE1 NE2 REMARK 470 GLU A 466 CG CD OE1 OE2 REMARK 470 GLN A 469 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 771 O HOH A 968 1.93 REMARK 500 O HOH A 746 O HOH A 960 1.96 REMARK 500 O HOH A 827 O HOH A 983 2.02 REMARK 500 O HOH A 943 O HOH T 104 2.10 REMARK 500 O HOH A 934 O HOH A 960 2.12 REMARK 500 O HOH A 941 O HOH A 960 2.12 REMARK 500 O HOH A 968 O HOH P 131 2.16 REMARK 500 O HOH P 112 O HOH P 125 2.17 REMARK 500 OP2 DG T 11 O HOH T 101 2.17 REMARK 500 O HOH A 940 O HOH A 943 2.18 REMARK 500 O HOH A 706 O HOH A 887 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 1 P DG D 1 OP3 -0.125 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT T 7 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 3.4 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 LEU A 254 -115.10 -153.91 REMARK 500 HIS A 255 -2.40 -140.35 REMARK 500 CYS A 300 -32.36 -172.05 REMARK 500 CYS A 415 -138.01 -112.92 REMARK 500 ARG A 438 -23.33 -145.04 REMARK 500 SER A 463 88.08 -168.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1007 DISTANCE = 6.36 ANGSTROMS 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 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 99.0 REMARK 620 3 ALA A 344 O 88.7 87.4 REMARK 620 4 HOH A 928 O 92.2 92.2 179.1 REMARK 620 5 DA P 5 OP1 161.1 99.4 88.2 91.0 REMARK 620 6 HOH P 107 O 75.8 173.9 89.2 91.2 85.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 94.7 REMARK 620 3 DCT A 601 O1A 95.2 95.4 REMARK 620 4 DCT A 601 O1B 171.5 88.4 92.4 REMARK 620 5 DCT A 601 O1G 89.2 174.7 87.7 87.2 REMARK 620 6 HOH A 804 O 86.8 89.4 174.6 85.3 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 604 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 463 O REMARK 620 2 HOH A 800 O 81.5 REMARK 620 3 HOH A 922 O 90.9 83.9 REMARK 620 4 HOH A 998 O 178.3 98.4 87.4 REMARK 620 5 HOH T 104 O 101.2 109.4 163.1 80.5 REMARK 620 6 HOH T 121 O 91.5 161.2 78.8 88.1 88.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCT A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5III RELATED DB: PDB REMARK 900 RELATED ID: 5IIK RELATED DB: PDB REMARK 900 RELATED ID: 5IIL RELATED DB: PDB REMARK 900 RELATED ID: 5IIM RELATED DB: PDB REMARK 900 RELATED ID: 5IIN RELATED DB: PDB REMARK 900 RELATED ID: 5IIO RELATED DB: PDB DBREF 5IIJ A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 5IIJ D 1 4 PDB 5IIJ 5IIJ 1 4 DBREF 5IIJ P 1 6 PDB 5IIJ 5IIJ 1 6 DBREF 5IIJ T 1 11 PDB 5IIJ 5IIJ 1 11 SEQRES 1 A 334 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 334 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 334 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 334 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 334 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 334 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 334 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 334 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 334 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 334 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 334 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 334 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 334 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 334 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 334 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 334 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 334 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 334 SER GLN GLU GLU ASN GLY GLN GLN GLN LYS TYR LEU GLY SEQRES 19 A 334 VAL CYS ARG LEU PRO GLY PRO GLY ARG ARG HIS ARG ARG SEQRES 20 A 334 LEU ASP ILE ILE VAL VAL PRO TYR SER GLU PHE ALA CYS SEQRES 21 A 334 ALA LEU LEU TYR PHE THR GLY SER ALA HIS PHE ASN ARG SEQRES 22 A 334 SER MET ARG ALA LEU ALA LYS THR LYS GLY MET SER LEU SEQRES 23 A 334 SER GLU HIS ALA LEU SER THR ALA VAL VAL ARG ASN THR SEQRES 24 A 334 HIS GLY CYS LYS VAL GLY PRO GLY ARG VAL LEU PRO THR SEQRES 25 A 334 PRO THR GLU LYS ASP VAL PHE ARG LEU LEU GLY LEU PRO SEQRES 26 A 334 TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 D 4 DG DC DC DG SEQRES 1 P 6 DC DA DG DT DA DOC SEQRES 1 T 11 DC DG DG DC 8OG DG DT DA DC DT DG HET DOC P 6 18 HET 8OG T 5 23 HET DCT A 601 27 HET MG A 602 1 HET NA A 603 1 HET NA A 604 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 DOC C9 H14 N3 O6 P FORMUL 4 8OG C10 H14 N5 O8 P FORMUL 5 DCT C9 H16 N3 O12 P3 FORMUL 6 MG MG 2+ FORMUL 7 NA 2(NA 1+) FORMUL 9 HOH *409(H2 O) HELIX 1 AA1 HIS A 255 GLN A 270 1 16 HELIX 2 AA2 ASP A 272 PHE A 289 1 18 HELIX 3 AA3 GLY A 306 GLY A 320 1 15 HELIX 4 AA4 LEU A 322 ILE A 328 5 7 HELIX 5 AA5 SER A 331 ASN A 340 1 10 HELIX 6 AA6 GLY A 345 GLN A 355 1 11 HELIX 7 AA7 SER A 359 ALA A 367 1 9 HELIX 8 AA8 THR A 370 HIS A 379 1 10 HELIX 9 AA9 HIS A 379 GLU A 385 1 7 HELIX 10 AB1 ARG A 389 ALA A 405 1 17 HELIX 11 AB2 CYS A 415 ARG A 420 1 6 HELIX 12 AB3 ILE A 443 GLU A 454 1 12 HELIX 13 AB4 PRO A 495 SER A 497 5 3 HELIX 14 AB5 GLU A 498 GLY A 508 1 11 HELIX 15 AB6 SER A 509 LYS A 523 1 15 HELIX 16 AB7 THR A 555 LEU A 563 1 9 HELIX 17 AB8 GLU A 569 ASP A 574 5 6 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ASP A 490 N VAL A 430 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N TYR A 473 O ILE A 491 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N VAL A 462 O LEU A 474 SHEET 1 AA3 2 MET A 525 LEU A 527 0 SHEET 2 AA3 2 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 LINK O3' DA P 5 P DOC P 6 1555 1555 1.60 LINK O3' DC T 4 P 8OG T 5 1555 1555 1.61 LINK O3' 8OG T 5 P DG T 6 1555 1555 1.61 LINK O SER A 339 NA NA A 603 1555 1555 2.29 LINK O ILE A 341 NA NA A 603 1555 1555 2.42 LINK O ALA A 344 NA NA A 603 1555 1555 2.30 LINK OD1 ASP A 427 MG MG A 602 1555 1555 2.05 LINK OD2 ASP A 429 MG MG A 602 1555 1555 2.08 LINK O SER A 463 NA NA A 604 1555 1555 2.36 LINK O1A DCT A 601 MG MG A 602 1555 1555 2.05 LINK O1B DCT A 601 MG MG A 602 1555 1555 2.06 LINK O1G DCT A 601 MG MG A 602 1555 1555 2.12 LINK MG MG A 602 O HOH A 804 1555 1555 2.12 LINK NA NA A 603 O HOH A 928 1555 1555 2.36 LINK NA NA A 603 OP1 DA P 5 1555 1555 2.49 LINK NA NA A 603 O HOH P 107 1555 1555 2.61 LINK NA NA A 604 O HOH A 800 1555 1555 2.52 LINK NA NA A 604 O HOH A 922 1555 1555 2.46 LINK NA NA A 604 O HOH A 998 1555 1555 2.47 LINK NA NA A 604 O HOH T 104 1555 1555 2.40 LINK NA NA A 604 O HOH T 121 1555 1555 2.57 CISPEP 1 ASN A 253 LEU A 254 0 -7.94 CISPEP 2 GLY A 508 SER A 509 0 3.56 SITE 1 AC1 22 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC1 22 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC1 22 PHE A 506 ALA A 510 ASN A 513 MG A 602 SITE 4 AC1 22 HOH A 705 HOH A 715 HOH A 781 HOH A 794 SITE 5 AC1 22 HOH A 804 HOH A 815 HOH A 865 DOC P 6 SITE 6 AC1 22 HOH P 114 8OG T 5 SITE 1 AC2 4 ASP A 427 ASP A 429 DCT A 601 HOH A 804 SITE 1 AC3 6 SER A 339 ILE A 341 ALA A 344 HOH A 928 SITE 2 AC3 6 DA P 5 HOH P 107 SITE 1 AC4 6 SER A 463 HOH A 800 HOH A 922 HOH A 998 SITE 2 AC4 6 HOH T 104 HOH T 121 CRYST1 55.749 62.850 140.076 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 0.017938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007139 0.00000