HEADER HYDROLASE/RNA 25-JUN-14 4QPX TITLE NV POLYMERASE POST-INCORPORATION-LIKE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 331-838; COMPND 5 SYNONYM: POLYPROTEIN; COMPND 6 EC: 2.7.7.48; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'); COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: RNA OLIGONUCLEOTIDE; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3'); COMPND 15 CHAIN: T; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: RNA OLIGONUCLEOTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NORWALK VIRUS; SOURCE 3 ORGANISM_TAXID: 11983; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 MOL_ID: 3; SOURCE 9 SYNTHETIC: YES KEYWDS RNA-DEPEDENT RNA POLYMERASE, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.F.ZAMYATKIN,F.PARRA,P.GROCHULSKI,K.K.S.NG REVDAT 2 20-SEP-23 4QPX 1 REMARK SEQADV LINK REVDAT 1 22-APR-15 4QPX 0 JRNL AUTH D.ZAMYATKIN,C.RAO,E.HOFFARTH,G.JURCA,H.RHO,F.PARRA, JRNL AUTH 2 P.GROCHULSKI,K.K.NG JRNL TITL STRUCTURE OF A BACKTRACKED STATE REVEALS CONFORMATIONAL JRNL TITL 2 CHANGES SIMILAR TO THE STATE FOLLOWING NUCLEOTIDE JRNL TITL 3 INCORPORATION IN HUMAN NOROVIRUS POLYMERASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 3099 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25478829 JRNL DOI 10.1107/S1399004714021518 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2684 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3660 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 192 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3884 REMARK 3 NUCLEIC ACID ATOMS : 317 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.96000 REMARK 3 B22 (A**2) : 0.96000 REMARK 3 B33 (A**2) : -1.93000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.714 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4357 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5964 ; 1.119 ; 2.068 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 493 ; 5.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;34.280 ;23.795 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 687 ;13.193 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.326 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 662 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3166 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2478 ; 1.704 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4012 ; 2.663 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1879 ; 3.885 ; 3.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1952 ; 5.044 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 8 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : T 101 T 126 REMARK 3 RESIDUE RANGE : P 201 P 221 REMARK 3 RESIDUE RANGE : A 701 A 978 REMARK 3 RESIDUE RANGE : P 101 P 101 REMARK 3 RESIDUE RANGE : A 601 A 604 REMARK 3 RESIDUE RANGE : T 2 T 8 REMARK 3 RESIDUE RANGE : P 1 P 8 REMARK 3 RESIDUE RANGE : A 4 A 505 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9678 30.2401 -2.3730 REMARK 3 T TENSOR REMARK 3 T11: 0.0652 T22: 0.0749 REMARK 3 T33: 0.1084 T12: -0.0011 REMARK 3 T13: -0.0372 T23: 0.0434 REMARK 3 L TENSOR REMARK 3 L11: 0.1526 L22: 1.2357 REMARK 3 L33: 0.8680 L12: -0.0705 REMARK 3 L13: 0.0630 L23: -0.3225 REMARK 3 S TENSOR REMARK 3 S11: 0.0813 S12: -0.0254 S13: -0.0155 REMARK 3 S21: -0.1818 S22: 0.0048 S23: 0.1368 REMARK 3 S31: 0.0598 S32: -0.0317 S33: -0.0861 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000086364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 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 : SI(111) REMARK 200 OPTICS : MIRRORS 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73009 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.84900 REMARK 200 R SYM FOR SHELL (I) : 0.84900 REMARK 200 FOR SHELL : 1.820 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 3BSO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19 % PEG 8000, 25% GLYCEROL, 100 MM REMARK 280 TRIS-HCL, PH 7.0, 50 MM KCL, 10 MM MNCL2 AND 0.1% 2- REMARK 280 MECAPTOETHANOL , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 94.06500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.61000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.03250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.61000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.61000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 141.09750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.61000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.61000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.03250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.61000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.61000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 141.09750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 94.06500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 LYS A 467 REMARK 465 GLU A 468 REMARK 465 GLY A 469 REMARK 465 GLY A 470 REMARK 465 MET A 471 REMARK 465 ASP A 472 REMARK 465 PHE A 473 REMARK 465 GLU A 506 REMARK 465 ASP A 507 REMARK 465 GLY A 508 REMARK 465 VAL A 509 REMARK 465 GLU A 510 REMARK 465 U T 1 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 A T 2 P OP1 OP2 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 G T 8 O5' - C5' - C4' ANGL. DEV. = -4.8 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 ARG A 245 60.59 33.72 REMARK 500 HIS A 433 -167.38 -113.13 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 MN A 604 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 99 OD2 REMARK 620 2 GLU A 205 OE2 106.4 REMARK 620 3 HIS A 209 NE2 138.5 95.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 242 OD1 REMARK 620 2 ASP A 343 OD1 99.6 REMARK 620 3 ASP A 344 OD1 91.0 89.3 REMARK 620 4 G P 7 O3' 176.7 83.5 90.1 REMARK 620 5 G P 8 OP1 112.7 87.3 156.3 66.2 REMARK 620 6 HOH P 219 O 89.2 168.5 97.9 87.6 82.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 242 OD2 REMARK 620 2 TYR A 243 O 90.9 REMARK 620 3 ASP A 343 OD2 81.6 92.6 REMARK 620 4 HOH A 960 O 89.0 103.3 161.7 REMARK 620 5 G P 8 OP1 86.1 171.0 78.6 85.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BSO RELATED DB: PDB REMARK 900 NV POLYMERASE PRE-INCORPORATION COMPLEX REMARK 900 RELATED ID: 1SH0 RELATED DB: PDB REMARK 900 NV POLYMERASE APOENZYME DBREF 4QPX A 3 510 UNP Q70ET3 Q70ET3_9CALI 331 838 DBREF 4QPX P 1 8 PDB 4QPX 4QPX 1 8 DBREF 4QPX T 1 8 PDB 4QPX 4QPX 1 8 SEQADV 4QPX GLY A 1 UNP Q70ET3 EXPRESSION TAG SEQADV 4QPX SER A 2 UNP Q70ET3 EXPRESSION TAG SEQRES 1 A 510 GLY SER ASP SER LYS GLY THR TYR CYS GLY ALA PRO ILE SEQRES 2 A 510 LEU GLY PRO GLY SER ALA PRO LYS LEU SER THR LYS THR SEQRES 3 A 510 LYS PHE TRP ARG SER SER THR ALA PRO LEU PRO PRO GLY SEQRES 4 A 510 THR TYR GLU PRO ALA TYR LEU GLY GLY LYS ASP PRO ARG SEQRES 5 A 510 VAL LYS GLY GLY PRO SER LEU GLN GLN VAL MET ARG ASP SEQRES 6 A 510 GLN LEU LYS PRO PHE THR GLU PRO ARG GLY LYS PRO PRO SEQRES 7 A 510 LYS PRO SER VAL LEU GLU ALA ALA LYS LYS THR ILE ILE SEQRES 8 A 510 ASN VAL LEU GLU GLN THR ILE ASP PRO PRO ASP LYS TRP SEQRES 9 A 510 SER PHE ALA GLN ALA CYS ALA SER LEU ASP LYS THR THR SEQRES 10 A 510 SER SER GLY HIS PRO HIS HIS MET ARG LYS ASN ASP CYS SEQRES 11 A 510 TRP ASN GLY GLU SER PHE THR GLY LYS LEU ALA ASP GLN SEQRES 12 A 510 ALA SER LYS ALA ASN LEU MET PHE GLU GLU GLY LYS ASN SEQRES 13 A 510 MET THR PRO VAL TYR THR GLY ALA LEU LYS ASP GLU LEU SEQRES 14 A 510 VAL LYS THR ASP LYS ILE TYR GLY LYS ILE LYS LYS ARG SEQRES 15 A 510 LEU LEU TRP GLY SER ASP LEU ALA THR MET ILE ARG CYS SEQRES 16 A 510 ALA ARG ALA PHE GLY GLY LEU MET ASP GLU LEU LYS THR SEQRES 17 A 510 HIS CYS VAL THR LEU PRO ILE ARG VAL GLY MET ASN MET SEQRES 18 A 510 ASN GLU ASP GLY PRO ILE ILE PHE GLU ARG HIS SER ARG SEQRES 19 A 510 TYR ARG TYR HIS TYR ASP ALA ASP TYR SER ARG TRP ASP SEQRES 20 A 510 SER THR GLN GLN ARG ALA VAL LEU ALA ALA ALA LEU GLU SEQRES 21 A 510 ILE MET VAL LYS PHE SER SER GLU PRO HIS LEU ALA GLN SEQRES 22 A 510 VAL VAL ALA GLU ASP LEU LEU SER PRO SER VAL VAL ASP SEQRES 23 A 510 VAL GLY ASP PHE THR ILE SER ILE ASN GLU GLY LEU PRO SEQRES 24 A 510 SER GLY VAL PRO CYS THR SER GLN TRP ASN SER ILE ALA SEQRES 25 A 510 HIS TRP LEU LEU THR LEU CYS ALA LEU SER GLU VAL THR SEQRES 26 A 510 ASN LEU SER PRO ASP ILE ILE GLN ALA ASN SER LEU PHE SEQRES 27 A 510 SER PHE TYR GLY ASP ASP GLU ILE VAL SER THR ASP ILE SEQRES 28 A 510 LYS LEU ASP PRO GLU LYS LEU THR ALA LYS LEU LYS GLU SEQRES 29 A 510 TYR GLY LEU LYS PRO THR ARG PRO ASP LYS THR GLU GLY SEQRES 30 A 510 PRO LEU VAL ILE SER GLU ASP LEU ASN GLY LEU THR PHE SEQRES 31 A 510 LEU ARG ARG THR VAL THR ARG ASP PRO ALA GLY TRP PHE SEQRES 32 A 510 GLY LYS LEU GLU GLN SER SER ILE LEU ARG GLN MET TYR SEQRES 33 A 510 TRP THR ARG GLY PRO ASN HIS GLU ASP PRO SER GLU THR SEQRES 34 A 510 MET ILE PRO HIS SER GLN ARG PRO ILE GLN LEU MET SER SEQRES 35 A 510 LEU LEU GLY GLU ALA ALA LEU HIS GLY PRO ALA PHE TYR SEQRES 36 A 510 SER LYS ILE SER LYS LEU VAL ILE ALA GLU LEU LYS GLU SEQRES 37 A 510 GLY GLY MET ASP PHE TYR VAL PRO ARG GLN GLU PRO MET SEQRES 38 A 510 PHE ARG TRP MET ARG PHE SER ASP LEU SER THR TRP GLU SEQRES 39 A 510 GLY ASP ARG ASN LEU ALA PRO SER PHE VAL ASN GLU ASP SEQRES 40 A 510 GLY VAL GLU SEQRES 1 P 8 U G C C C G G G SEQRES 1 T 8 U A C C C G G G HET GOL A 601 6 HET MN A 602 1 HET MN A 603 1 HET MN A 604 1 HET GOL P 101 6 HETNAM GOL GLYCEROL HETNAM MN MANGANESE (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 2(C3 H8 O3) FORMUL 5 MN 3(MN 2+) FORMUL 9 HOH *325(H2 O) HELIX 1 1 SER A 58 GLU A 72 1 15 HELIX 2 2 LYS A 79 ILE A 98 1 20 HELIX 3 3 SER A 105 LEU A 113 1 9 HELIX 4 4 ARG A 126 TRP A 131 5 6 HELIX 5 5 THR A 137 GLY A 154 1 18 HELIX 6 6 THR A 172 GLY A 177 1 6 HELIX 7 7 ASP A 188 HIS A 209 1 22 HELIX 8 8 ASN A 220 ARG A 234 1 15 HELIX 9 9 TRP A 246 GLN A 250 5 5 HELIX 10 10 GLN A 251 SER A 266 1 16 HELIX 11 11 GLU A 268 SER A 281 1 14 HELIX 12 12 CYS A 304 ASN A 326 1 23 HELIX 13 13 SER A 328 ASN A 335 1 8 HELIX 14 14 ASP A 354 TYR A 365 1 12 HELIX 15 15 GLU A 407 ARG A 413 1 7 HELIX 16 16 GLN A 435 LEU A 449 1 15 HELIX 17 17 GLY A 451 ALA A 464 1 14 HELIX 18 18 ARG A 477 SER A 488 1 12 HELIX 19 19 ASP A 496 ALA A 500 5 5 SHEET 1 A 6 THR A 7 TYR A 8 0 SHEET 2 A 6 ALA A 11 PRO A 16 -1 O ALA A 11 N TYR A 8 SHEET 3 A 6 PHE A 290 ILE A 294 -1 O THR A 291 N LEU A 14 SHEET 4 A 6 SER A 283 ASP A 286 -1 N VAL A 285 O ILE A 292 SHEET 5 A 6 VAL A 160 LEU A 165 1 N TYR A 161 O ASP A 286 SHEET 6 A 6 LEU A 183 GLY A 186 -1 O LEU A 184 N ALA A 164 SHEET 1 B 2 THR A 26 ARG A 30 0 SHEET 2 B 2 TRP A 417 HIS A 423 -1 O THR A 418 N TRP A 29 SHEET 1 C 2 GLU A 42 PRO A 43 0 SHEET 2 C 2 LEU A 169 VAL A 170 -1 O VAL A 170 N GLU A 42 SHEET 1 D 4 SER A 336 TYR A 341 0 SHEET 2 D 4 ASP A 344 THR A 349 -1 O SER A 348 N LEU A 337 SHEET 3 D 4 TYR A 237 TYR A 243 -1 N TYR A 237 O THR A 349 SHEET 4 D 4 PRO A 369 THR A 370 -1 O THR A 370 N ASP A 242 SHEET 1 E 3 THR A 389 PHE A 390 0 SHEET 2 E 3 ARG A 393 ASP A 398 -1 O ARG A 393 N PHE A 390 SHEET 3 E 3 GLY A 401 LEU A 406 -1 O PHE A 403 N THR A 396 LINK OD2 ASP A 99 MN MN A 604 1555 1555 1.90 LINK OE2 GLU A 205 MN MN A 604 1555 1555 1.90 LINK NE2 HIS A 209 MN MN A 604 1555 1555 1.99 LINK OD1 ASP A 242 MN MN A 602 1555 1555 1.90 LINK OD2 ASP A 242 MN MN A 603 1555 1555 1.92 LINK O TYR A 243 MN MN A 603 1555 1555 1.93 LINK OD1 ASP A 343 MN MN A 602 1555 1555 1.93 LINK OD2 ASP A 343 MN MN A 603 1555 1555 1.92 LINK OD1 ASP A 344 MN MN A 602 1555 1555 1.92 LINK MN MN A 602 O3' G P 7 1555 1555 2.53 LINK MN MN A 602 OP1 G P 8 1555 1555 1.92 LINK MN MN A 602 O HOH P 219 1555 1555 2.33 LINK MN MN A 603 O HOH A 960 1555 1555 2.37 LINK MN MN A 603 OP1 G P 8 1555 1555 2.58 CISPEP 1 HIS A 121 PRO A 122 0 -3.75 SITE 1 AC1 9 VAL A 211 THR A 212 LEU A 213 PRO A 214 SITE 2 AC1 9 ARG A 216 ARG A 231 LEU A 337 PHE A 338 SITE 3 AC1 9 HOH A 742 SITE 1 AC2 7 ASP A 242 ASP A 343 ASP A 344 MN A 603 SITE 2 AC2 7 G P 7 G P 8 HOH P 219 SITE 1 AC3 6 ASP A 242 TYR A 243 ASP A 343 MN A 602 SITE 2 AC3 6 HOH A 960 G P 8 SITE 1 AC4 3 ASP A 99 GLU A 205 HIS A 209 SITE 1 AC5 10 LYS A 166 HOH A 934 G P 6 G P 7 SITE 2 AC5 10 HOH P 214 HOH P 216 HOH P 218 C T 3 SITE 3 AC5 10 C T 4 C T 5 CRYST1 81.220 81.220 188.130 90.00 90.00 90.00 P 41 21 2 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 0.012312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005315 0.00000