HEADER VIRAL PROTEIN 31-JUL-18 6H80 TITLE DENGUE-RDRP3-INHIBITOR COMPLEX CO-CRYSTALLISATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS TYPE 3 (STRAIN SRI SOURCE 3 LANKA/1266/2000); SOURCE 4 ORGANISM_COMMON: DENV-3; SOURCE 5 ORGANISM_TAXID: 408692; SOURCE 6 STRAIN: SRI LANKA/1266/2000; SOURCE 7 TISSUE: 866768; SOURCE 8 GENE: POL; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DENGUE VIRUS; CRYSTALLIZATION SCREEN; RNA-DEPENDENT RNA POLYMERASE; KEYWDS 2 FLAVIVIRUS; ANTIVIRAL DRUG-DISCOVERY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.K.TALAPATRA,F.KOZIELSKI REVDAT 2 17-JAN-24 6H80 1 REMARK REVDAT 1 13-MAR-19 6H80 0 JRNL AUTH F.RICCIO,S.K.TALAPATRA,S.OXENFORD,R.ANGELL,M.MAZZON, JRNL AUTH 2 F.KOZIELSKI JRNL TITL DEVELOPMENT AND VALIDATION OF RDRP SCREEN, A CRYSTALLIZATION JRNL TITL 2 SCREEN FOR VIRAL RNA-DEPENDENT RNA POLYMERASES. JRNL REF BIOL OPEN V. 8 2019 JRNL REFN ESSN 2046-6390 JRNL PMID 30602529 JRNL DOI 10.1242/BIO.037663 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39103 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1946 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 56.7535 - 5.5418 1.00 2845 143 0.1878 0.2019 REMARK 3 2 5.5418 - 4.3992 1.00 2711 129 0.1681 0.1866 REMARK 3 3 4.3992 - 3.8432 1.00 2680 129 0.1633 0.2209 REMARK 3 4 3.8432 - 3.4919 1.00 2648 147 0.1889 0.2550 REMARK 3 5 3.4919 - 3.2417 1.00 2655 131 0.1853 0.2332 REMARK 3 6 3.2417 - 3.0505 1.00 2658 137 0.1913 0.2232 REMARK 3 7 3.0505 - 2.8978 1.00 2627 139 0.1929 0.2764 REMARK 3 8 2.8978 - 2.7716 1.00 2646 140 0.1983 0.2795 REMARK 3 9 2.7716 - 2.6649 1.00 2614 136 0.2072 0.2601 REMARK 3 10 2.6649 - 2.5730 1.00 2640 150 0.2176 0.2993 REMARK 3 11 2.5730 - 2.4925 1.00 2620 130 0.2330 0.2916 REMARK 3 12 2.4925 - 2.4213 1.00 2583 153 0.2537 0.2920 REMARK 3 13 2.4213 - 2.3575 1.00 2608 156 0.2774 0.3180 REMARK 3 14 2.3575 - 2.3000 1.00 2622 126 0.3244 0.4001 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.80 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 : 0.012 4667 REMARK 3 ANGLE : 1.201 6316 REMARK 3 CHIRALITY : 0.062 669 REMARK 3 PLANARITY : 0.008 803 REMARK 3 DIHEDRAL : 8.102 3805 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 6H80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39134 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 52.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48200 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: 4HHJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0, 20% PEG 550 MME, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 82.54000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 82.54000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.62500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.96000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 82.54000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.62500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.96000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 82.54000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.62500 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 GLY A 266 REMARK 465 SER A 267 REMARK 465 HIS A 268 REMARK 465 MET A 269 REMARK 465 LEU A 270 REMARK 465 ASP A 271 REMARK 465 ALA A 312 REMARK 465 THR A 313 REMARK 465 GLY A 314 REMARK 465 SER A 315 REMARK 465 ALA A 316 REMARK 465 SER A 317 REMARK 465 SER A 318 REMARK 465 THR A 343 REMARK 465 ASP A 344 REMARK 465 THR A 345 REMARK 465 THR A 346 REMARK 465 PRO A 347 REMARK 465 PHE A 348 REMARK 465 GLY A 349 REMARK 465 GLN A 350 REMARK 465 GLN A 351 REMARK 465 ARG A 352 REMARK 465 VAL A 353 REMARK 465 PHE A 354 REMARK 465 ALA A 406 REMARK 465 ALA A 407 REMARK 465 MET A 408 REMARK 465 GLY A 409 REMARK 465 ALA A 410 REMARK 465 VAL A 411 REMARK 465 PHE A 412 REMARK 465 THR A 413 REMARK 465 GLU A 414 REMARK 465 GLU A 415 REMARK 465 ASN A 416 REMARK 465 GLN A 417 REMARK 465 TRP A 418 REMARK 465 MET A 454 REMARK 465 GLY A 455 REMARK 465 LYS A 456 REMARK 465 ARG A 457 REMARK 465 GLU A 458 REMARK 465 LYS A 459 REMARK 465 LYS A 460 REMARK 465 LEU A 461 REMARK 465 GLY A 462 REMARK 465 GLU A 463 REMARK 465 PHE A 464 REMARK 465 GLY A 465 REMARK 465 LYS A 466 REMARK 465 ALA A 467 REMARK 465 LYS A 468 REMARK 465 GLY A 469 REMARK 465 ARG A 581 REMARK 465 PRO A 582 REMARK 465 THR A 583 REMARK 465 PRO A 584 REMARK 465 THR A 585 REMARK 465 GLY A 586 REMARK 465 PRO A 884 REMARK 465 SER A 885 REMARK 465 MET A 886 REMARK 465 LYS A 887 REMARK 465 ARG A 888 REMARK 465 PHE A 889 REMARK 465 ARG A 890 REMARK 465 LYS A 891 REMARK 465 GLU A 892 REMARK 465 GLU A 893 REMARK 465 GLU A 894 REMARK 465 SER A 895 REMARK 465 GLU A 896 REMARK 465 GLY A 897 REMARK 465 ALA A 898 REMARK 465 ILE A 899 REMARK 465 TRP A 900 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 ASP A 274 OD1 OD2 REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 SER A 289 OG REMARK 470 ASP A 295 CG OD1 OD2 REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 VAL A 310 CG1 CG2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 LYS A 355 CD CE NZ REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 LYS A 400 CD CE NZ REMARK 470 ASP A 419 CG OD1 OD2 REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 LYS A 445 CG CD CE NZ REMARK 470 TYR A 451 CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL A 480 CG1 CG2 REMARK 470 LYS A 641 CG CD CE NZ REMARK 470 GLN A 645 CD OE1 NE2 REMARK 470 LYS A 698 CG CD CE NZ REMARK 470 GLU A 825 CG CD OE1 OE2 REMARK 470 GLU A 834 CD OE1 OE2 REMARK 470 LYS A 841 CG CD CE NZ REMARK 470 GLN A 868 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 CD2 HIS A 712 ZN ZN A 1003 1.22 REMARK 500 OE2 GLU A 509 O HOH A 1101 1.30 REMARK 500 OD1 ASP A 664 O HOH A 1102 1.35 REMARK 500 NE2 HIS A 712 ZN ZN A 1003 1.37 REMARK 500 NE2 HIS A 714 ZN ZN A 1003 1.53 REMARK 500 OE2 GLU A 437 OG SER A 448 1.64 REMARK 500 OE1 GLU A 484 OH TYR A 572 1.70 REMARK 500 OE1 GLU A 437 N GLY A 447 1.78 REMARK 500 ND1 HIS A 495 O HOH A 1103 1.81 REMARK 500 NZ LYS A 371 O LEU A 638 1.83 REMARK 500 OE1 GLU A 507 O HOH A 1103 1.87 REMARK 500 CD2 HIS A 712 NE2 HIS A 714 2.08 REMARK 500 OE1 GLU A 437 N SER A 448 2.14 REMARK 500 NE2 HIS A 712 CB CYS A 728 2.18 REMARK 500 CD2 HIS A 441 O HOH A 1151 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CG2 VAL A 333 CG2 VAL A 333 3654 1.82 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 GLU A 437 CD GLU A 437 OE1 -0.086 REMARK 500 GLU A 437 CD GLU A 437 OE2 -0.117 REMARK 500 HIS A 441 CE1 HIS A 441 NE2 -0.094 REMARK 500 GLU A 549 CD GLU A 549 OE1 -0.068 REMARK 500 GLU A 653 CD GLU A 653 OE1 -0.069 REMARK 500 HIS A 712 CE1 HIS A 712 NE2 -0.125 REMARK 500 HIS A 714 CE1 HIS A 714 NE2 -0.088 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 GLU A 437 N - CA - CB ANGL. DEV. = 11.6 DEGREES REMARK 500 GLU A 437 CB - CG - CD ANGL. DEV. = 21.5 DEGREES REMARK 500 GLU A 437 OE1 - CD - OE2 ANGL. DEV. = -9.3 DEGREES REMARK 500 HIS A 441 CB - CA - C ANGL. DEV. = 19.1 DEGREES REMARK 500 HIS A 441 CA - CB - CG ANGL. DEV. = 14.7 DEGREES REMARK 500 CYS A 446 CB - CA - C ANGL. DEV. = 7.6 DEGREES REMARK 500 CYS A 449 CB - CA - C ANGL. DEV. = 15.2 DEGREES REMARK 500 CYS A 449 CA - CB - SG ANGL. DEV. = 11.3 DEGREES REMARK 500 ASN A 452 CB - CA - C ANGL. DEV. = -13.8 DEGREES REMARK 500 HIS A 712 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 HIS A 712 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 HIS A 712 ND1 - CG - CD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 HIS A 714 CB - CA - C ANGL. DEV. = 17.0 DEGREES REMARK 500 HIS A 714 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 CYS A 728 CB - CA - C ANGL. DEV. = 10.1 DEGREES REMARK 500 CYS A 728 N - CA - CB ANGL. DEV. = 11.6 DEGREES REMARK 500 CYS A 728 CA - CB - SG ANGL. DEV. = 16.5 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 THR A 290 60.30 -155.48 REMARK 500 TYR A 503 -50.80 74.87 REMARK 500 GLN A 597 171.28 82.55 REMARK 500 SER A 791 149.30 85.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 419 SER A 420 -31.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 361 0.29 SIDE CHAIN REMARK 500 ARG A 364 0.15 SIDE CHAIN REMARK 500 ARG A 389 0.08 SIDE CHAIN REMARK 500 ARG A 395 0.22 SIDE CHAIN REMARK 500 ARG A 403 0.13 SIDE CHAIN REMARK 500 ARG A 436 0.21 SIDE CHAIN REMARK 500 ARG A 471 0.23 SIDE CHAIN REMARK 500 ARG A 561 0.21 SIDE CHAIN REMARK 500 ARG A 594 0.20 SIDE CHAIN REMARK 500 ARG A 739 0.08 SIDE CHAIN REMARK 500 ARG A 773 0.09 SIDE CHAIN REMARK 500 ARG A 792 0.15 SIDE CHAIN REMARK 500 ARG A 815 0.10 SIDE CHAIN REMARK 500 ARG A 842 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS A 547 10.72 REMARK 500 VAL A 785 10.33 REMARK 500 HIS A 786 10.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 CYS A 449 SG 132.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 728 SG REMARK 620 2 CYS A 847 SG 121.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5V5 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1008 DBREF 6H80 A 272 900 UNP Q6YMS4 POLG_DEN3S 2762 3390 SEQADV 6H80 GLY A 266 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H80 SER A 267 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H80 HIS A 268 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H80 MET A 269 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H80 LEU A 270 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H80 ASP A 271 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H80 LEU A 366 UNP Q6YMS4 MET 2856 VARIANT SEQADV 6H80 VAL A 372 UNP Q6YMS4 ALA 2862 VARIANT SEQADV 6H80 VAL A 480 UNP Q6YMS4 ALA 2970 VARIANT SEQADV 6H80 VAL A 603 UNP Q6YMS4 LEU 3093 VARIANT SEQRES 1 A 635 GLY SER HIS MET LEU ASP ASN MET ASP VAL ILE GLY GLU SEQRES 2 A 635 ARG ILE LYS ARG ILE LYS GLU GLU HIS ASN SER THR TRP SEQRES 3 A 635 HIS TYR ASP ASP GLU ASN PRO TYR LYS THR TRP ALA TYR SEQRES 4 A 635 HIS GLY SER TYR GLU VAL LYS ALA THR GLY SER ALA SER SEQRES 5 A 635 SER MET ILE ASN GLY VAL VAL LYS LEU LEU THR LYS PRO SEQRES 6 A 635 TRP ASP VAL VAL PRO MET VAL THR GLN MET ALA MET THR SEQRES 7 A 635 ASP THR THR PRO PHE GLY GLN GLN ARG VAL PHE LYS GLU SEQRES 8 A 635 LYS VAL ASP THR ARG THR PRO ARG PRO LEU PRO GLY THR SEQRES 9 A 635 ARG LYS VAL MET GLU ILE THR ALA GLU TRP LEU TRP ARG SEQRES 10 A 635 THR LEU GLY ARG ASN LYS ARG PRO ARG LEU CYS THR ARG SEQRES 11 A 635 GLU GLU PHE THR LYS LYS VAL ARG THR ASN ALA ALA MET SEQRES 12 A 635 GLY ALA VAL PHE THR GLU GLU ASN GLN TRP ASP SER ALA SEQRES 13 A 635 LYS ALA ALA VAL GLU ASP GLU GLU PHE TRP LYS LEU VAL SEQRES 14 A 635 ASP ARG GLU ARG GLU LEU HIS LYS LEU GLY LYS CYS GLY SEQRES 15 A 635 SER CYS VAL TYR ASN MET MET GLY LYS ARG GLU LYS LYS SEQRES 16 A 635 LEU GLY GLU PHE GLY LYS ALA LYS GLY SER ARG ALA ILE SEQRES 17 A 635 TRP TYR MET TRP LEU GLY VAL ARG TYR LEU GLU PHE GLU SEQRES 18 A 635 ALA LEU GLY PHE LEU ASN GLU ASP HIS TRP PHE SER ARG SEQRES 19 A 635 GLU ASN SER TYR SER GLY VAL GLU GLY GLU GLY LEU HIS SEQRES 20 A 635 LYS LEU GLY TYR ILE LEU ARG ASP ILE SER LYS ILE PRO SEQRES 21 A 635 GLY GLY ALA MET TYR ALA ASP ASP THR ALA GLY TRP ASP SEQRES 22 A 635 THR ARG ILE THR GLU ASP ASP LEU HIS ASN GLU GLU LYS SEQRES 23 A 635 ILE ILE GLN GLN MET ASP PRO GLU HIS ARG GLN LEU ALA SEQRES 24 A 635 ASN ALA ILE PHE LYS LEU THR TYR GLN ASN LYS VAL VAL SEQRES 25 A 635 LYS VAL GLN ARG PRO THR PRO THR GLY THR VAL MET ASP SEQRES 26 A 635 ILE ILE SER ARG LYS ASP GLN ARG GLY SER GLY GLN VAL SEQRES 27 A 635 GLY THR TYR GLY LEU ASN THR PHE THR ASN MET GLU ALA SEQRES 28 A 635 GLN LEU VAL ARG GLN MET GLU GLY GLU GLY VAL LEU THR SEQRES 29 A 635 LYS ALA ASP LEU GLU ASN PRO HIS LEU LEU GLU LYS LYS SEQRES 30 A 635 ILE THR GLN TRP LEU GLU THR LYS GLY VAL GLU ARG LEU SEQRES 31 A 635 LYS ARG MET ALA ILE SER GLY ASP ASP CYS VAL VAL LYS SEQRES 32 A 635 PRO ILE ASP ASP ARG PHE ALA ASN ALA LEU LEU ALA LEU SEQRES 33 A 635 ASN ASP MET GLY LYS VAL ARG LYS ASP ILE PRO GLN TRP SEQRES 34 A 635 GLN PRO SER LYS GLY TRP HIS ASP TRP GLN GLN VAL PRO SEQRES 35 A 635 PHE CYS SER HIS HIS PHE HIS GLU LEU ILE MET LYS ASP SEQRES 36 A 635 GLY ARG LYS LEU VAL VAL PRO CYS ARG PRO GLN ASP GLU SEQRES 37 A 635 LEU ILE GLY ARG ALA ARG ILE SER GLN GLY ALA GLY TRP SEQRES 38 A 635 SER LEU ARG GLU THR ALA CYS LEU GLY LYS ALA TYR ALA SEQRES 39 A 635 GLN MET TRP SER LEU MET TYR PHE HIS ARG ARG ASP LEU SEQRES 40 A 635 ARG LEU ALA SER ASN ALA ILE CYS SER ALA VAL PRO VAL SEQRES 41 A 635 HIS TRP VAL PRO THR SER ARG THR THR TRP SER ILE HIS SEQRES 42 A 635 ALA HIS HIS GLN TRP MET THR THR GLU ASP MET LEU THR SEQRES 43 A 635 VAL TRP ASN ARG VAL TRP ILE GLU GLU ASN PRO TRP MET SEQRES 44 A 635 GLU ASP LYS THR PRO VAL THR THR TRP GLU ASN VAL PRO SEQRES 45 A 635 TYR LEU GLY LYS ARG GLU ASP GLN TRP CYS GLY SER LEU SEQRES 46 A 635 ILE GLY LEU THR SER ARG ALA THR TRP ALA GLN ASN ILE SEQRES 47 A 635 PRO THR ALA ILE GLN GLN VAL ARG SER LEU ILE GLY ASN SEQRES 48 A 635 GLU GLU PHE LEU ASP TYR MET PRO SER MET LYS ARG PHE SEQRES 49 A 635 ARG LYS GLU GLU GLU SER GLU GLY ALA ILE TRP HET 5V5 A1001 17 HET ZN A1002 1 HET ZN A1003 1 HET PEG A1004 7 HET PEG A1005 7 HET PEG A1006 7 HET PEG A1007 7 HET PEG A1008 7 HETNAM 5V5 2-(4-METHOXY-3-THIOPHEN-2-YL-PHENYL)ETHANOIC ACID HETNAM ZN ZINC ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 5V5 C13 H12 O3 S FORMUL 3 ZN 2(ZN 2+) FORMUL 5 PEG 5(C4 H10 O3) FORMUL 10 HOH *164(H2 O) HELIX 1 AA1 ASN A 272 HIS A 287 1 16 HELIX 2 AA2 ASN A 321 LEU A 327 1 7 HELIX 3 AA3 THR A 328 VAL A 333 5 6 HELIX 4 AA4 VAL A 334 MET A 342 1 9 HELIX 5 AA5 LEU A 366 GLY A 385 1 20 HELIX 6 AA6 THR A 394 THR A 404 1 11 HELIX 7 AA7 ALA A 421 GLU A 426 1 6 HELIX 8 AA8 ASP A 427 LYS A 442 1 16 HELIX 9 AA9 ALA A 472 GLY A 489 1 18 HELIX 10 AB1 GLY A 489 ASP A 494 1 6 HELIX 11 AB2 SER A 498 TYR A 503 1 6 HELIX 12 AB3 GLY A 510 ILE A 524 1 15 HELIX 13 AB4 GLY A 536 ILE A 541 5 6 HELIX 14 AB5 THR A 542 GLU A 550 1 9 HELIX 15 AB6 LYS A 551 MET A 556 5 6 HELIX 16 AB7 ASP A 557 TYR A 572 1 16 HELIX 17 AB8 GLY A 604 GLU A 625 1 22 HELIX 18 AB9 THR A 629 ASN A 635 1 7 HELIX 19 AC1 GLU A 640 LYS A 656 1 17 HELIX 20 AC2 ASP A 671 ALA A 677 5 7 HELIX 21 AC3 LEU A 678 MET A 684 1 7 HELIX 22 AC4 ASP A 702 VAL A 706 5 5 HELIX 23 AC5 PRO A 730 ARG A 739 1 10 HELIX 24 AC6 SER A 747 TYR A 766 1 20 HELIX 25 AC7 ARG A 769 VAL A 783 1 15 HELIX 26 AC8 ASP A 808 ILE A 818 1 11 HELIX 27 AC9 THR A 832 VAL A 836 5 5 HELIX 28 AD1 GLY A 840 CYS A 847 1 8 HELIX 29 AD2 LEU A 853 GLY A 875 1 23 SHEET 1 AA1 4 ALA A 303 GLU A 309 0 SHEET 2 AA1 4 VAL A 588 ARG A 594 -1 O SER A 593 N ALA A 303 SHEET 3 AA1 4 LYS A 575 VAL A 579 -1 N VAL A 577 O ILE A 592 SHEET 4 AA1 4 TYR A 451 ASN A 452 1 N TYR A 451 O VAL A 576 SHEET 1 AA2 2 MET A 658 SER A 661 0 SHEET 2 AA2 2 ASP A 664 VAL A 667 -1 O ASP A 664 N SER A 661 SHEET 1 AA3 2 HIS A 712 ILE A 717 0 SHEET 2 AA3 2 LYS A 723 CYS A 728 -1 O CYS A 728 N HIS A 712 LINK SG CYS A 446 ZN ZN A1002 1555 1555 2.36 LINK SG CYS A 449 ZN ZN A1002 1555 1555 1.93 LINK SG CYS A 728 ZN ZN A1003 1555 1555 2.91 LINK SG CYS A 847 ZN ZN A1003 1555 1555 2.46 SITE 1 AC1 10 CYS A 709 HIS A 711 ARG A 729 THR A 794 SITE 2 AC1 10 SER A 796 HIS A 798 ALA A 799 TRP A 803 SITE 3 AC1 10 HOH A1116 HOH A1160 SITE 1 AC2 3 GLU A 437 CYS A 446 CYS A 449 SITE 1 AC3 4 HIS A 712 HIS A 714 CYS A 728 CYS A 847 SITE 1 AC4 2 TRP A 694 ASP A 826 SITE 1 AC5 2 ASP A 435 ASN A 635 SITE 1 AC6 2 PRO A 822 TRP A 823 SITE 1 AC7 3 ARG A 654 ARG A 657 HOH A1218 SITE 1 AC8 2 SER A 710 TRP A 846 CRYST1 165.080 181.250 57.920 90.00 90.00 90.00 C 2 2 21 8 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 0.006058 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017265 0.00000