HEADER TRANSFERASE 06-SEP-12 4GZK TITLE STRUCTURE AND INTERACTIONS OF THE RNA-DEPENDENT RNA POLYMERASE FROM TITLE 2 BACTERIOPHAGE PHI12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DEPENDENT RNA POLYMERASE P2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE PHI12; SOURCE 3 ORGANISM_TAXID: 161736; SOURCE 4 GENE: P2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPG27 KEYWDS RNA-DIRECTED RNA POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.REN,M.FRANKLIN,R.GHOSE REVDAT 3 28-FEB-24 4GZK 1 REMARK SEQADV LINK REVDAT 2 18-SEP-13 4GZK 1 JRNL REVDAT 1 24-JUL-13 4GZK 0 JRNL AUTH Z.REN,M.C FRANKLIN,R.GHOSE JRNL TITL STRUCTURE OF THE RNA-DIRECTED RNA POLYMERASE FROM THE JRNL TITL 2 CYSTOVIRUS 12. JRNL REF PROTEINS V. 81 1479 2013 JRNL REFN ISSN 0887-3585 JRNL PMID 23568335 JRNL DOI 10.1002/PROT.24297 REMARK 2 REMARK 2 RESOLUTION. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 105419 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5224 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6946 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 362 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 1166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.22000 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): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.661 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5465 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3800 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7414 ; 1.533 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9190 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 668 ; 5.865 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 281 ;32.147 ;23.559 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 913 ;11.661 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;19.364 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 773 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6150 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1190 ; 0.001 ; 0.020 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): 3279 ; 1.529 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1316 ; 0.467 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5304 ; 2.496 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2186 ; 3.969 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2100 ; 5.982 ; 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): 9265 ; 1.599 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4GZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-12 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 : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105656 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 M NA FORMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 67.40250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 67.40250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.16000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1069 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 PRO A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 GLU A 6 REMARK 465 SER A 7 REMARK 465 PRO A 8 REMARK 465 LYS A 9 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 826 O HOH A 1844 1.97 REMARK 500 O HOH A 1027 O HOH A 1777 1.97 REMARK 500 O HOH A 834 O HOH A 1845 1.99 REMARK 500 O HOH A 1118 O HOH A 1956 2.02 REMARK 500 ND2 ASN A 253 O HOH A 1184 2.03 REMARK 500 O HOH A 1186 O HOH A 1672 2.03 REMARK 500 O HOH A 1007 O HOH A 1949 2.04 REMARK 500 O HOH A 1243 O HOH A 1906 2.05 REMARK 500 O HOH A 912 O HOH A 1949 2.05 REMARK 500 O HOH A 1089 O HOH A 1934 2.07 REMARK 500 O HOH A 1216 O HOH A 1922 2.07 REMARK 500 O HOH A 1111 O HOH A 1949 2.08 REMARK 500 O HOH A 1327 O HOH A 1959 2.08 REMARK 500 O HOH A 1367 O HOH A 1937 2.08 REMARK 500 O HOH A 1597 O HOH A 1919 2.11 REMARK 500 O HOH A 1315 O HOH A 1938 2.12 REMARK 500 CD2 LEU A 298 O HOH A 1936 2.14 REMARK 500 O HOH A 1484 O HOH A 1778 2.15 REMARK 500 O HOH A 1878 O HOH A 1888 2.15 REMARK 500 O HOH A 1261 O HOH A 1879 2.15 REMARK 500 O HOH A 1193 O HOH A 1909 2.16 REMARK 500 O HOH A 1342 O HOH A 1776 2.16 REMARK 500 O HOH A 1763 O HOH A 1911 2.17 REMARK 500 O HOH A 1154 O HOH A 1914 2.17 REMARK 500 O HOH A 1523 O HOH A 1837 2.17 REMARK 500 O HOH A 1135 O HOH A 1953 2.17 REMARK 500 O HOH A 869 O HOH A 1733 2.18 REMARK 500 O HOH A 1162 O HOH A 1778 2.19 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 GLN A 73 CG GLN A 73 CD 0.142 REMARK 500 GLU A 379 CG GLU A 379 CD 0.100 REMARK 500 GLU A 494 CD GLU A 494 OE1 0.072 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 ASP A 128 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 164 CG - CD - NE ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 164 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 469 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 470 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG A 496 NE - CZ - NH1 ANGL. DEV. = 3.3 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 GLU A 12 128.17 -37.22 REMARK 500 THR A 17 -158.34 -98.23 REMARK 500 HIS A 330 50.47 -154.44 REMARK 500 ARG A 408 50.05 -110.30 REMARK 500 ASP A 616 83.59 -152.41 REMARK 500 HIS A 622 -18.64 -147.98 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 MG A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 269 OE1 REMARK 620 2 GLU A 269 OE2 46.9 REMARK 620 3 HOH A1093 O 86.5 97.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 704 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 348 O REMARK 620 2 ASP A 470 OD1 140.0 REMARK 620 3 GLU A 503 OE2 101.7 117.0 REMARK 620 4 HOH A 960 O 73.0 85.9 107.1 REMARK 620 5 HOH A 972 O 82.8 93.9 107.8 140.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 626 O REMARK 620 2 ILE A 629 O 83.1 REMARK 620 3 HOH A1406 O 99.6 91.5 REMARK 620 4 HOH A1611 O 101.9 102.8 155.5 REMARK 620 5 HOH A1697 O 163.5 113.4 81.0 75.1 REMARK 620 6 HOH A1779 O 84.2 167.1 92.4 78.0 79.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 931 O REMARK 620 2 HOH A1104 O 88.2 REMARK 620 3 HOH A1215 O 84.5 171.4 REMARK 620 4 HOH A1246 O 80.6 99.1 84.1 REMARK 620 5 HOH A1586 O 153.1 88.4 100.1 73.6 REMARK 620 6 HOH A1789 O 105.2 86.3 91.3 172.3 101.2 REMARK 620 7 HOH A1939 O 60.7 119.3 52.9 122.0 141.6 58.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 706 DBREF 4GZK A 1 659 UNP Q94M06 Q94M06_9VIRU 1 659 SEQADV 4GZK ALA A 2 UNP Q94M06 MET 2 ENGINEERED MUTATION SEQRES 1 A 659 MET ALA PRO THR ASN GLU SER PRO LYS HIS ALA GLU THR SEQRES 2 A 659 ARG ILE VAL THR ASP ALA PRO ARG ASN SER GLU SER VAL SEQRES 3 A 659 GLY ASP HIS LEU PHE ASN GLY GLY VAL ASN HIS HIS ASP SEQRES 4 A 659 GLU ASP PRO ASP ALA TYR THR LYS MET TYR GLY PRO LEU SEQRES 5 A 659 VAL GLY TYR ASP PRO ARG ASN PRO THR THR LEU PHE ALA SEQRES 6 A 659 ASN ALA ARG GLN THR GLY THR GLN LEU VAL ALA PRO ARG SEQRES 7 A 659 LYS ALA ARG GLU ILE LEU THR GLY ILE TYR SER PHE GLU SEQRES 8 A 659 PRO THR VAL LEU ALA PHE GLN ARG GLU PHE VAL LYS ARG SEQRES 9 A 659 ALA ASN ALA VAL ALA GLN PRO ASP LEU ASN SER ASP GLY SEQRES 10 A 659 PHE SER LEU ASN GLY LEU HIS THR THR PHE ASP SER ILE SEQRES 11 A 659 ARG SER VAL SER GLY TYR PRO GLN TRP PRO VAL SER ALA SEQRES 12 A 659 LEU PRO LYS SER ASN VAL GLY LEU LEU ARG ASP LEU LYS SEQRES 13 A 659 LEU GLN GLU ARG MET THR ALA ARG GLN VAL VAL ILE ALA SEQRES 14 A 659 ARG GLU ILE TRP LYS ARG VAL TRP GLY HIS MET LYS PRO SEQRES 15 A 659 THR ALA ILE LYS ILE PRO LYS MET SER THR SER GLY PRO SEQRES 16 A 659 PRO ARG ASN VAL ASN ASP ALA GLU MET LYS LEU GLN TYR SEQRES 17 A 659 ALA LEU ALA LEU PHE SER GLY ASN ARG TYR ASN GLY TYR SEQRES 18 A 659 LEU ASP ALA PHE LYS SER GLY ASP LEU SER ARG PHE TYR SEQRES 19 A 659 ARG ASP TYR GLU ALA ALA VAL ILE MET GLY THR ASN VAL SEQRES 20 A 659 ARG TRP GLN VAL ASP ASN PRO GLY LYS LYS ARG ASP TYR SEQRES 21 A 659 TRP ALA GLN ALA ASP ILE GLU ARG GLU LEU ALA PRO SER SEQRES 22 A 659 LYS ARG PRO ILE THR THR LYS VAL GLU ILE ASN GLY THR SEQRES 23 A 659 VAL TYR ASP ASP PHE ALA ALA MET ARG THR ARG LEU VAL SEQRES 24 A 659 ASN ALA GLY PRO TRP THR ILE ASN VAL ALA LEU GLN PRO SEQRES 25 A 659 PHE ALA THR GLY CYS MET ASN ALA MET PHE GLU LEU TYR SEQRES 26 A 659 ARG ALA THR TRP HIS PRO ASP GLU ASP LYS ILE ALA GLY SEQRES 27 A 659 PHE LEU GLU GLY LYS HIS ALA PHE PHE GLY ASP VAL SER SEQRES 28 A 659 SER TYR ASP HIS SER PHE SER GLU GLU LYS ILE ASP LEU SEQRES 29 A 659 SER LEU GLU VAL GLY LYS GLU PHE ILE SER PRO GLU ILE SEQRES 30 A 659 MET GLU LEU ALA SER SER LEU PHE TYR ALA ALA TYR PHE SEQRES 31 A 659 THR ARG PRO LEU GLY PRO ASP ASP GLY PRO GLN LEU VAL SEQRES 32 A 659 GLY ASN PRO ASN ARG TYR LEU GLU LYS GLN VAL LYS ALA SEQRES 33 A 659 GLY ASN ARG SER GLY HIS ALA PHE THR SER LEU PHE ALA SEQRES 34 A 659 LYS VAL TRP LYS VAL ILE ASP THR VAL SER LYS PHE ASP SEQRES 35 A 659 GLN MET GLY TYR ASP VAL VAL ALA ASN MET ASP ALA ILE SEQRES 36 A 659 LEU LYS GLY ASP MET PRO PHE GLY CYS ILE ASN ASN GLY SEQRES 37 A 659 ASP ASP GLU ILE VAL TRP PHE LYS SER GLU ARG ASP TYR SEQRES 38 A 659 ARG LEU PHE LEU ARG LEU LEU GLU THR GLN PRO GLN GLU SEQRES 39 A 659 GLN ARG MET PHE LYS VAL GLY PRO GLU GLU GLY ALA VAL SEQRES 40 A 659 PHE SER GLY SER VAL TYR GLN LEU ILE GLY PRO LEU LYS SEQRES 41 A 659 TYR GLN ALA VAL GLU ARG ILE THR THR PRO PHE GLN ARG SEQRES 42 A 659 ILE ILE CYS PRO GLU ARG SER ILE GLY GLY ASN PHE ARG SEQRES 43 A 659 LYS PHE TRP PRO LEU GLY ILE LEU GLU ARG TYR ASN LYS SEQRES 44 A 659 ARG ASN SER HIS PRO VAL LEU GLU GLU VAL TRP ARG VAL SEQRES 45 A 659 PHE ASP ASP THR TYR ALA THR LEU MET GLU PRO HIS TYR SEQRES 46 A 659 GLY SER PHE LEU GLY ILE VAL GLN ARG ALA HIS LYS GLU SEQRES 47 A 659 ILE PRO PHE SER VAL ASP ASP LEU SER TRP LYS GLU ILE SEQRES 48 A 659 MET VAL LEU ASP ASP PRO ASN LYS MET TYR HIS ARG PHE SEQRES 49 A 659 THR ASP GLU GLU ILE ARG ASP GLN VAL GLN GLU SER ALA SEQRES 50 A 659 PHE ARG LYS LEU GLN PRO ILE PHE PHE GLU ARG MET PHE SEQRES 51 A 659 LYS GLU HIS TYR LYS GLY ASN TYR VAL HET MG A 701 1 HET MG A 702 1 HET MG A 703 1 HET MG A 704 1 HET MG A 705 1 HET FMT A 706 3 HETNAM MG MAGNESIUM ION HETNAM FMT FORMIC ACID FORMUL 2 MG 5(MG 2+) FORMUL 7 FMT C H2 O2 FORMUL 8 HOH *1166(H2 O) HELIX 1 1 SER A 25 HIS A 29 5 5 HELIX 2 2 ASN A 36 ASP A 41 1 6 HELIX 3 3 ASP A 43 TYR A 49 1 7 HELIX 4 4 ASN A 59 ALA A 65 5 7 HELIX 5 5 GLU A 91 ALA A 109 1 19 HELIX 6 6 PHE A 127 ILE A 130 5 4 HELIX 7 7 ASN A 148 LEU A 155 1 8 HELIX 8 8 THR A 162 GLY A 178 1 17 HELIX 9 9 ASP A 201 PHE A 213 1 13 HELIX 10 10 ASN A 216 SER A 227 1 12 HELIX 11 11 ASP A 229 GLU A 238 1 10 HELIX 12 12 ALA A 262 GLU A 269 1 8 HELIX 13 13 PRO A 303 TYR A 325 1 23 HELIX 14 14 TYR A 325 HIS A 330 1 6 HELIX 15 15 ASP A 332 ASP A 334 5 3 HELIX 16 16 LYS A 335 LEU A 340 1 6 HELIX 17 17 TYR A 353 PHE A 357 5 5 HELIX 18 18 SER A 358 LYS A 370 1 13 HELIX 19 19 SER A 374 TYR A 386 1 13 HELIX 20 20 ASN A 405 TYR A 409 5 5 HELIX 21 21 PHE A 424 GLY A 445 1 22 HELIX 22 22 ASN A 451 LYS A 457 1 7 HELIX 23 23 SER A 477 GLN A 491 1 15 HELIX 24 24 PRO A 492 ARG A 496 5 5 HELIX 25 25 THR A 528 CYS A 536 1 9 HELIX 26 26 TRP A 549 LYS A 559 1 11 HELIX 27 27 ARG A 560 SER A 562 5 3 HELIX 28 28 HIS A 563 MET A 581 1 19 HELIX 29 29 MET A 581 GLY A 586 1 6 HELIX 30 30 SER A 587 GLU A 598 1 12 HELIX 31 31 SER A 602 LEU A 606 5 5 HELIX 32 32 SER A 607 ASP A 616 1 10 HELIX 33 33 PRO A 617 TYR A 621 5 5 HELIX 34 34 THR A 625 ILE A 629 5 5 HELIX 35 35 ARG A 630 ALA A 637 1 8 HELIX 36 36 GLN A 642 PHE A 645 5 4 HELIX 37 37 PHE A 646 TYR A 654 1 9 SHEET 1 A 2 GLU A 82 LEU A 84 0 SHEET 2 A 2 ILE A 87 TYR A 88 -1 O ILE A 87 N LEU A 84 SHEET 1 B 3 SER A 132 PRO A 137 0 SHEET 2 B 3 ALA A 292 ALA A 301 1 O MET A 294 N TYR A 136 SHEET 3 B 3 GLY A 244 GLN A 250 -1 N ASN A 246 O VAL A 299 SHEET 1 C 2 HIS A 179 MET A 180 0 SHEET 2 C 2 ASN A 657 TYR A 658 1 O ASN A 657 N MET A 180 SHEET 1 D 2 ILE A 185 PRO A 188 0 SHEET 2 D 2 PHE A 638 LEU A 641 -1 O ARG A 639 N ILE A 187 SHEET 1 E 2 ASP A 259 TYR A 260 0 SHEET 2 E 2 ARG A 275 PRO A 276 -1 O ARG A 275 N TYR A 260 SHEET 1 F 2 GLU A 282 ILE A 283 0 SHEET 2 F 2 THR A 286 VAL A 287 -1 O THR A 286 N ILE A 283 SHEET 1 G 4 PHE A 462 ASN A 467 0 SHEET 2 G 4 ASP A 470 PHE A 475 -1 O ASP A 470 N ASN A 467 SHEET 3 G 4 HIS A 344 SER A 351 -1 N PHE A 346 O VAL A 473 SHEET 4 G 4 LYS A 499 PRO A 502 -1 O GLY A 501 N ASP A 349 SHEET 1 H 2 TYR A 389 THR A 391 0 SHEET 2 H 2 GLN A 401 VAL A 403 -1 O VAL A 403 N TYR A 389 SHEET 1 I 3 VAL A 507 PHE A 508 0 SHEET 2 I 3 SER A 511 GLY A 517 -1 O SER A 511 N PHE A 508 SHEET 3 I 3 LYS A 520 GLU A 525 -1 O VAL A 524 N VAL A 512 LINK OD2 ASP A 28 MG MG A 705 1555 1555 2.63 LINK OE1 GLU A 269 MG MG A 701 1555 1555 2.63 LINK OE2 GLU A 269 MG MG A 701 1555 1555 2.82 LINK O GLY A 348 MG MG A 704 1555 1555 2.30 LINK OD1 ASP A 470 MG MG A 704 1555 1555 2.07 LINK OE2 GLU A 503 MG MG A 704 1555 1555 2.03 LINK O ASP A 626 MG MG A 702 1555 1555 2.22 LINK O ILE A 629 MG MG A 702 1555 1555 2.27 LINK MG MG A 701 O HOH A1093 1555 1555 2.40 LINK MG MG A 702 O HOH A1406 1555 1555 2.40 LINK MG MG A 702 O HOH A1611 1555 1555 2.45 LINK MG MG A 702 O HOH A1697 1555 1555 2.68 LINK MG MG A 702 O HOH A1779 1555 1555 2.68 LINK MG MG A 703 O HOH A 931 1555 1555 2.52 LINK MG MG A 703 O HOH A1104 1555 1555 2.36 LINK MG MG A 703 O HOH A1215 1555 1555 2.44 LINK MG MG A 703 O HOH A1246 1555 1555 2.44 LINK MG MG A 703 O HOH A1586 1555 1555 2.87 LINK MG MG A 703 O HOH A1789 1555 1555 2.08 LINK MG MG A 703 O HOH A1939 1555 1555 2.73 LINK MG MG A 704 O HOH A 960 1555 1555 2.61 LINK MG MG A 704 O HOH A 972 1555 1555 2.55 CISPEP 1 TRP A 139 PRO A 140 0 -14.09 CISPEP 2 PRO A 195 PRO A 196 0 5.39 SITE 1 AC1 5 GLU A 269 ASP A 442 GLY A 445 TYR A 446 SITE 2 AC1 5 HOH A1093 SITE 1 AC2 6 ASP A 626 ILE A 629 HOH A1406 HOH A1611 SITE 2 AC2 6 HOH A1697 HOH A1779 SITE 1 AC3 8 LYS A 280 HOH A 931 HOH A1104 HOH A1215 SITE 2 AC3 8 HOH A1246 HOH A1586 HOH A1789 HOH A1939 SITE 1 AC4 5 GLY A 348 ASP A 470 GLU A 503 HOH A 960 SITE 2 AC4 5 HOH A 972 SITE 1 AC5 3 ASP A 28 ARG A 571 ASP A 574 SITE 1 AC6 7 ARG A 164 ASP A 447 VAL A 448 VAL A 449 SITE 2 AC6 7 ALA A 450 HOH A1808 HOH A1946 CRYST1 134.805 72.320 96.828 90.00 90.00 90.00 P 21 21 2 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 0.007418 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010328 0.00000