HEADER TRANSFERASE 02-APR-09 3A1G TITLE HIGH-RESOLUTION CRYSTAL STRUCTURE OF RNA POLYMERASE PB1-PB2 SUBUNITS TITLE 2 FROM INFLUENZA A VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: PB1 C-TERMINAL FRAGMENT, UNP RESIDUES 678-757; COMPND 5 SYNONYM: POLYMERASE BASIC PROTEIN 1, PB1, RNA-DIRECTED RNA POLYMERASE COMPND 6 SUBUNIT P1; COMPND 7 EC: 2.7.7.48; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: POLYMERASE BASIC PROTEIN 2; COMPND 11 CHAIN: B, D; COMPND 12 FRAGMENT: PB2 N-TERMINAL RAGMENT, UNP RESIDUES 1-37; COMPND 13 SYNONYM: RNA POLYMERASE PB2 SUBUNIT, RNA-DIRECTED RNA POLYMERASE COMPND 14 SUBUNIT P3; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (A/PUERTO RICO/8/34(H1N1)); SOURCE 3 ORGANISM_TAXID: 211044; SOURCE 4 STRAIN: STRAIN A/PUERTO RICO/8/1934 H1N1; SOURCE 5 GENE: PB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RILCODONPLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS (A/PUERTO RICO/8/34(H1N1)); SOURCE 13 ORGANISM_TAXID: 211044; SOURCE 14 STRAIN: STRAIN A/PUERTO RICO/8/1934 H1N1; SOURCE 15 GENE: PB2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RILCODONPLUS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: MIDIFIED PET28 KEYWDS INFLUENZA VIRUS, RNA POLYMERASE, NUCLEOTIDE-BINDING, KEYWDS 2 NUCLEOTIDYLTRANSFERASE, NUCLEUS, RNA REPLICATION, RNA-DIRECTED RNA KEYWDS 3 POLYMERASE, TRANSFERASE, MITOCHONDRION, MRNA CAPPING, MRNA KEYWDS 4 PROCESSING, VIRION EXPDTA X-RAY DIFFRACTION AUTHOR K.SUGIYAMA,S.-Y.PARK,E.OBAYASHI REVDAT 4 15-NOV-23 3A1G 1 REMARK REVDAT 3 01-NOV-23 3A1G 1 SEQADV LINK REVDAT 2 07-JUL-09 3A1G 1 JRNL REVDAT 1 09-JUN-09 3A1G 0 JRNL AUTH K.SUGIYAMA,E.OBAYASHI,A.KAWAGUCHI,Y.SUZUKI,J.R.H.TAME, JRNL AUTH 2 K.NAGATA,S.-Y.PARK JRNL TITL STRUCTURAL INSIGHT INTO THE ESSENTIAL PB1-PB2 SUBUNIT JRNL TITL 2 CONTACT OF THE INFLUENZA VIRUS RNA POLYMERASE JRNL REF EMBO J. V. 28 1803 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19461581 JRNL DOI 10.1038/EMBOJ.2009.138 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24512 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1315 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1399 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.34000 REMARK 3 B22 (A**2) : -2.46000 REMARK 3 B33 (A**2) : -1.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.70000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.709 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1844 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2448 ; 1.845 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 6.734 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 88 ;37.835 ;22.045 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 400 ;18.170 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;18.653 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 268 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1332 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 948 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1291 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 85 ; 0.158 ; 0.200 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): 50 ; 0.226 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.264 ; 0.200 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): 1152 ; 1.503 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1792 ; 2.164 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 777 ; 3.729 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 656 ; 4.906 ; 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 : NULL 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 : 1.20 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 3A1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000028691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-09 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.0000 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) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 25.00 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 2ZTT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 80MM SODIUM CITRATE, 20% PEG 4000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 30.35050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.99350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.35050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.99350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 678 REMARK 465 GLN A 679 REMARK 465 ARG A 680 REMARK 465 GLY A 681 REMARK 465 VAL A 682 REMARK 465 LEU A 683 REMARK 465 GLU A 684 REMARK 465 SER B 36 REMARK 465 GLY B 37 REMARK 465 SER C 678 REMARK 465 GLN C 679 REMARK 465 ARG C 680 REMARK 465 GLY C 681 REMARK 465 VAL C 682 REMARK 465 LEU C 683 REMARK 465 GLU C 684 REMARK 465 SER D 36 REMARK 465 GLY D 37 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 CYS A 693 CB CYS A 693 SG -0.096 REMARK 500 MSE B 1 SE MSE B 1 CE -0.427 REMARK 500 GLU B 2 CB GLU B 2 CG 0.122 REMARK 500 GLU B 2 CG GLU B 2 CD 0.107 REMARK 500 CYS C 693 CB CYS C 693 SG -0.107 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 MSE A 718 CG - SE - CE ANGL. DEV. = -19.9 DEGREES REMARK 500 LEU B 10 CB - CG - CD1 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG C 723 NE - CZ - NH2 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 SER A 703 57.07 -60.77 REMARK 500 TYR A 705 57.49 -92.60 REMARK 500 ARG C 706 98.07 -68.30 REMARK 500 ILE D 30 -70.06 -51.26 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 SER A 703 SER A 704 -147.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZTT RELATED DB: PDB DBREF 3A1G A 678 757 UNP P03431 RDRP_I34A1 678 757 DBREF 3A1G B 1 37 UNP P03428 PB2_I34A1 1 37 DBREF 3A1G C 678 757 UNP P03431 RDRP_I34A1 678 757 DBREF 3A1G D 1 37 UNP P03428 PB2_I34A1 1 37 SEQADV 3A1G GLY B -2 UNP P03428 EXPRESSION TAG SEQADV 3A1G GLY B -1 UNP P03428 EXPRESSION TAG SEQADV 3A1G SER B 0 UNP P03428 EXPRESSION TAG SEQADV 3A1G GLY D -2 UNP P03428 EXPRESSION TAG SEQADV 3A1G GLY D -1 UNP P03428 EXPRESSION TAG SEQADV 3A1G SER D 0 UNP P03428 EXPRESSION TAG SEQRES 1 A 80 SER GLN ARG GLY VAL LEU GLU ASP GLU GLN MSE TYR GLN SEQRES 2 A 80 ARG CYS CYS ASN LEU PHE GLU LYS PHE PHE PRO SER SER SEQRES 3 A 80 SER TYR ARG ARG PRO VAL GLY ILE SER SER MSE VAL GLU SEQRES 4 A 80 ALA MSE VAL SER ARG ALA ARG ILE ASP ALA ARG ILE ASP SEQRES 5 A 80 PHE GLU SER GLY ARG ILE LYS LYS GLU GLU PHE THR GLU SEQRES 6 A 80 ILE MSE LYS ILE CYS SER THR ILE GLU GLU LEU ARG ARG SEQRES 7 A 80 GLN LYS SEQRES 1 B 40 GLY GLY SER MSE GLU ARG ILE LYS GLU LEU ARG ASN LEU SEQRES 2 B 40 MSE SER GLN SER ARG THR ARG GLU ILE LEU THR LYS THR SEQRES 3 B 40 THR VAL ASP HIS MSE ALA ILE ILE LYS LYS TYR THR SER SEQRES 4 B 40 GLY SEQRES 1 C 80 SER GLN ARG GLY VAL LEU GLU ASP GLU GLN MSE TYR GLN SEQRES 2 C 80 ARG CYS CYS ASN LEU PHE GLU LYS PHE PHE PRO SER SER SEQRES 3 C 80 SER TYR ARG ARG PRO VAL GLY ILE SER SER MSE VAL GLU SEQRES 4 C 80 ALA MSE VAL SER ARG ALA ARG ILE ASP ALA ARG ILE ASP SEQRES 5 C 80 PHE GLU SER GLY ARG ILE LYS LYS GLU GLU PHE THR GLU SEQRES 6 C 80 ILE MSE LYS ILE CYS SER THR ILE GLU GLU LEU ARG ARG SEQRES 7 C 80 GLN LYS SEQRES 1 D 40 GLY GLY SER MSE GLU ARG ILE LYS GLU LEU ARG ASN LEU SEQRES 2 D 40 MSE SER GLN SER ARG THR ARG GLU ILE LEU THR LYS THR SEQRES 3 D 40 THR VAL ASP HIS MSE ALA ILE ILE LYS LYS TYR THR SER SEQRES 4 D 40 GLY MODRES 3A1G MSE A 688 MET SELENOMETHIONINE MODRES 3A1G MSE A 714 MET SELENOMETHIONINE MODRES 3A1G MSE A 718 MET SELENOMETHIONINE MODRES 3A1G MSE A 744 MET SELENOMETHIONINE MODRES 3A1G MSE B 1 MET SELENOMETHIONINE MODRES 3A1G MSE B 11 MET SELENOMETHIONINE MODRES 3A1G MSE B 28 MET SELENOMETHIONINE MODRES 3A1G MSE C 688 MET SELENOMETHIONINE MODRES 3A1G MSE C 714 MET SELENOMETHIONINE MODRES 3A1G MSE C 718 MET SELENOMETHIONINE MODRES 3A1G MSE C 744 MET SELENOMETHIONINE MODRES 3A1G MSE D 1 MET SELENOMETHIONINE MODRES 3A1G MSE D 11 MET SELENOMETHIONINE MODRES 3A1G MSE D 28 MET SELENOMETHIONINE HET MSE A 688 8 HET MSE A 714 8 HET MSE A 718 8 HET MSE A 744 8 HET MSE B 1 8 HET MSE B 11 8 HET MSE B 28 8 HET MSE C 688 8 HET MSE C 714 8 HET MSE C 718 8 HET MSE C 744 8 HET MSE D 1 8 HET MSE D 11 8 HET MSE D 28 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 5 HOH *63(H2 O) HELIX 1 1 GLU A 686 PHE A 700 1 15 HELIX 2 2 SER A 713 SER A 732 1 20 HELIX 3 3 LYS A 736 GLN A 756 1 21 HELIX 4 4 GLY B -2 MSE B 11 1 14 HELIX 5 5 GLN B 13 THR B 23 1 11 HELIX 6 6 ASP B 26 TYR B 34 1 9 HELIX 7 7 ASP C 685 PHE C 700 1 16 HELIX 8 8 SER C 713 SER C 732 1 20 HELIX 9 9 LYS C 736 GLN C 756 1 21 HELIX 10 10 GLY D -2 MSE D 11 1 14 HELIX 11 11 GLN D 13 THR D 23 1 11 HELIX 12 12 ASP D 26 TYR D 34 1 9 LINK C GLN A 687 N MSE A 688 1555 1555 1.34 LINK C MSE A 688 N TYR A 689 1555 1555 1.34 LINK C SER A 713 N MSE A 714 1555 1555 1.33 LINK C MSE A 714 N VAL A 715 1555 1555 1.33 LINK C ALA A 717 N MSE A 718 1555 1555 1.34 LINK C MSE A 718 N VAL A 719 1555 1555 1.33 LINK C ILE A 743 N MSE A 744 1555 1555 1.34 LINK C MSE A 744 N LYS A 745 1555 1555 1.33 LINK C SER B 0 N MSE B 1 1555 1555 1.34 LINK C MSE B 1 N GLU B 2 1555 1555 1.35 LINK C LEU B 10 N MSE B 11 1555 1555 1.31 LINK C MSE B 11 N SER B 12 1555 1555 1.33 LINK C HIS B 27 N MSE B 28 1555 1555 1.35 LINK C MSE B 28 N ALA B 29 1555 1555 1.33 LINK C GLN C 687 N MSE C 688 1555 1555 1.34 LINK C MSE C 688 N TYR C 689 1555 1555 1.33 LINK C SER C 713 N MSE C 714 1555 1555 1.33 LINK C MSE C 714 N VAL C 715 1555 1555 1.33 LINK C ALA C 717 N MSE C 718 1555 1555 1.32 LINK C MSE C 718 N VAL C 719 1555 1555 1.33 LINK C ILE C 743 N MSE C 744 1555 1555 1.35 LINK C MSE C 744 N LYS C 745 1555 1555 1.34 LINK C SER D 0 N MSE D 1 1555 1555 1.34 LINK C MSE D 1 N GLU D 2 1555 1555 1.33 LINK C LEU D 10 N MSE D 11 1555 1555 1.33 LINK C MSE D 11 N SER D 12 1555 1555 1.34 LINK C HIS D 27 N MSE D 28 1555 1555 1.35 LINK C MSE D 28 N ALA D 29 1555 1555 1.33 CRYST1 60.701 69.987 61.348 90.00 97.94 90.00 C 1 2 1 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 0.016474 0.000000 0.002297 0.00000 SCALE2 0.000000 0.014288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016458 0.00000