HEADER TRANSFERASE 21-AUG-11 3VGU TITLE E134A MUTANT NUCLEOSIDE DIPHOSPHATE KINASE DERIVED FROM HALOMONAS SP. TITLE 2 593 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 SYNONYM: NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOMONAS; SOURCE 3 ORGANISM_TAXID: 195704; SOURCE 4 STRAIN: 593; SOURCE 5 GENE: NDK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS HALOPHILIC, KINASE, FERREDOXIN FOLD, ATP-BINDING, NUCLEOTIDE-BINDING, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.OKAZAKI,Y.YONEZAWA,S.ARAI,F.MATSUMOTO,T.TAMADA,H.TOKUNAGA, AUTHOR 2 M.ISHIBASHI,M.TOKUNAGA,R.KUROKI REVDAT 2 08-NOV-23 3VGU 1 SEQADV REVDAT 1 11-JUL-12 3VGU 0 JRNL AUTH S.ARAI,Y.YONEZAWA,N.OKAZAKI,F.MATSUMOTO,T.TAMADA,H.TOKUNAGA, JRNL AUTH 2 M.ISHIBASHI,M.BLABER,M.TOKUNAGA,R.KUROKI JRNL TITL A STRUCTURAL MECHANISM FOR DIMERIC TO TETRAMERIC OLIGOMER JRNL TITL 2 CONVERSION IN HALOMONAS SP. NUCLEOSIDE DIPHOSPHATE KINASE JRNL REF PROTEIN SCI. V. 21 498 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22275000 JRNL DOI 10.1002/PRO.2032 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 47181 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2402 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2930 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 141 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8462 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 432 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.81000 REMARK 3 B22 (A**2) : 2.45000 REMARK 3 B33 (A**2) : -1.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.251 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.267 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8588 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11587 ; 1.630 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1109 ; 5.189 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 407 ;36.608 ;24.939 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1453 ;15.089 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 55 ;18.435 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1286 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6603 ; 0.008 ; 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): 5548 ; 1.194 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8826 ; 2.145 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3040 ; 3.259 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2761 ; 5.288 ; 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 : 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 4 REMARK 4 3VGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000095027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47185 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 90.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.25100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1NHK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.18M CALCIUM ACETATE HYDRATE, 0.09M REMARK 280 SODIUM CACODYLATE TRIHYDRATE, 16% PEG 8000, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 93.24450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.57450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 93.24450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.57450 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, 3, 4 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: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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: 3 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: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, G 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: 4 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: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, H 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 MET A 1 REMARK 465 MET B 1 REMARK 465 MET C 1 REMARK 465 MET D 1 REMARK 465 MET E 1 REMARK 465 MET F 1 REMARK 465 MET G 1 REMARK 465 MET H 1 REMARK 465 ARG H 57 REMARK 465 PRO H 58 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 G 45 CB GLU G 45 CG 0.127 REMARK 500 GLU G 45 CG GLU G 45 CD 0.108 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 LEU F 40 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG G 26 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ALA A 115 -42.11 70.26 REMARK 500 ALA B 37 143.59 -171.74 REMARK 500 ALA B 115 -46.82 62.74 REMARK 500 CYS B 139 78.93 -119.58 REMARK 500 ALA C 37 139.17 -175.93 REMARK 500 GLN C 109 -82.67 -75.08 REMARK 500 SER C 110 -169.79 -119.39 REMARK 500 ALA C 115 -47.31 65.87 REMARK 500 CYS C 139 79.06 -113.65 REMARK 500 GLU D 53 -18.42 -49.86 REMARK 500 PHE D 59 -0.87 -58.14 REMARK 500 ALA D 113 68.96 -108.10 REMARK 500 ALA D 115 -45.22 67.99 REMARK 500 CYS D 139 79.89 -102.21 REMARK 500 ALA E 37 149.23 -171.78 REMARK 500 ASN E 81 54.94 24.36 REMARK 500 ALA E 113 73.47 -105.58 REMARK 500 ALA E 115 -37.71 65.45 REMARK 500 CYS E 139 78.96 -113.18 REMARK 500 ALA F 37 141.50 -170.57 REMARK 500 ALA F 115 -42.74 64.61 REMARK 500 CYS F 139 71.25 -108.64 REMARK 500 ALA G 37 148.00 -177.33 REMARK 500 GLN G 109 -84.00 -73.84 REMARK 500 ALA G 115 -44.97 64.27 REMARK 500 ALA H 115 -48.89 66.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VGS RELATED DB: PDB REMARK 900 RELATED ID: 3VGT RELATED DB: PDB REMARK 900 RELATED ID: 3VGV RELATED DB: PDB DBREF 3VGU A 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU B 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU C 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU D 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU E 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU F 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU G 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 DBREF 3VGU H 1 141 UNP Q83WH5 Q83WH5_9GAMM 1 141 SEQADV 3VGU ALA A 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA B 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA C 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA D 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA E 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA F 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA G 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQADV 3VGU ALA H 134 UNP Q83WH5 GLU 134 ENGINEERED MUTATION SEQRES 1 A 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 A 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 A 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 A 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 A 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 A 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 A 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 A 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 A 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 A 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 A 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 B 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 B 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 B 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 B 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 B 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 B 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 B 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 B 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 B 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 B 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 B 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 C 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 C 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 C 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 C 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 C 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 C 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 C 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 C 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 C 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 C 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 C 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 D 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 D 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 D 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 D 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 D 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 D 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 D 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 D 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 D 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 D 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 D 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 E 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 E 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 E 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 E 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 E 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 E 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 E 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 E 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 E 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 E 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 E 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 F 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 F 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 F 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 F 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 F 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 F 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 F 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 F 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 F 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 F 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 F 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 G 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 G 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 G 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 G 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 G 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 G 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 G 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 G 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 G 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 G 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 G 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG SEQRES 1 H 141 MET ALA THR GLU ARG THR LEU SER ILE ILE LYS PRO ASP SEQRES 2 H 141 ALA VAL ALA LYS ASN VAL ILE GLY GLU ILE GLU SER ARG SEQRES 3 H 141 PHE GLU LYS ALA GLY LEU LYS ILE VAL ALA ALA LYS MET SEQRES 4 H 141 LEU GLN LEU SER GLN GLU GLN ALA GLU GLY PHE TYR ALA SEQRES 5 H 141 GLU HIS LYS GLU ARG PRO PHE PHE GLY ASP LEU VAL GLY SEQRES 6 H 141 PHE MET THR SER GLY PRO VAL VAL VAL GLN VAL LEU GLU SEQRES 7 H 141 GLY GLU ASN ALA ILE ALA ALA ASN ARG ASP LEU MET GLY SEQRES 8 H 141 ALA THR ASN PRO LYS GLU ALA GLU ALA GLY THR ILE ARG SEQRES 9 H 141 ALA ASP TYR ALA GLN SER ILE ASP ALA ASN ALA VAL HIS SEQRES 10 H 141 GLY SER ASP SER PRO GLU SER ALA ALA ARG GLU ILE ALA SEQRES 11 H 141 TYR PHE PHE ALA GLU SER GLU ILE CYS SER ARG FORMUL 9 HOH *432(H2 O) HELIX 1 1 LYS A 11 LYS A 17 1 7 HELIX 2 2 VAL A 19 ALA A 30 1 12 HELIX 3 3 SER A 43 TYR A 51 1 9 HELIX 4 4 ALA A 52 LYS A 55 5 4 HELIX 5 5 PHE A 59 THR A 68 1 10 HELIX 6 6 ASN A 81 GLY A 91 1 11 HELIX 7 7 ASN A 94 ALA A 98 5 5 HELIX 8 8 THR A 102 ALA A 108 1 7 HELIX 9 9 SER A 121 PHE A 133 1 13 HELIX 10 10 ALA A 134 ILE A 138 5 5 HELIX 11 11 LYS B 11 LYS B 17 1 7 HELIX 12 12 VAL B 19 ALA B 30 1 12 HELIX 13 13 SER B 43 TYR B 51 1 9 HELIX 14 14 ALA B 52 LYS B 55 5 4 HELIX 15 15 PHE B 59 THR B 68 1 10 HELIX 16 16 ASN B 81 GLY B 91 1 11 HELIX 17 17 ASN B 94 ALA B 98 5 5 HELIX 18 18 THR B 102 ALA B 108 1 7 HELIX 19 19 SER B 121 PHE B 133 1 13 HELIX 20 20 ALA B 134 ILE B 138 5 5 HELIX 21 21 LYS C 11 LYS C 17 1 7 HELIX 22 22 VAL C 19 ALA C 30 1 12 HELIX 23 23 SER C 43 TYR C 51 1 9 HELIX 24 24 ALA C 52 LYS C 55 5 4 HELIX 25 25 PHE C 59 MET C 67 1 9 HELIX 26 26 ASN C 81 GLY C 91 1 11 HELIX 27 27 ASN C 94 ALA C 98 5 5 HELIX 28 28 THR C 102 ALA C 108 1 7 HELIX 29 29 SER C 121 PHE C 133 1 13 HELIX 30 30 ALA C 134 ILE C 138 5 5 HELIX 31 31 LYS D 11 LYS D 17 1 7 HELIX 32 32 VAL D 19 ALA D 30 1 12 HELIX 33 33 SER D 43 TYR D 51 1 9 HELIX 34 34 ALA D 52 LYS D 55 5 4 HELIX 35 35 PHE D 59 SER D 69 1 11 HELIX 36 36 ASN D 81 GLY D 91 1 11 HELIX 37 37 THR D 102 ALA D 108 1 7 HELIX 38 38 SER D 121 PHE D 133 1 13 HELIX 39 39 ALA D 134 ILE D 138 5 5 HELIX 40 40 LYS E 11 LYS E 17 1 7 HELIX 41 41 VAL E 19 ALA E 30 1 12 HELIX 42 42 SER E 43 TYR E 51 1 9 HELIX 43 43 ALA E 52 LYS E 55 5 4 HELIX 44 44 PHE E 59 THR E 68 1 10 HELIX 45 45 ASN E 81 GLY E 91 1 11 HELIX 46 46 ASN E 94 ALA E 98 5 5 HELIX 47 47 THR E 102 ALA E 108 1 7 HELIX 48 48 SER E 121 PHE E 133 1 13 HELIX 49 49 ALA E 134 ILE E 138 5 5 HELIX 50 50 LYS F 11 LYS F 17 1 7 HELIX 51 51 VAL F 19 ALA F 30 1 12 HELIX 52 52 SER F 43 TYR F 51 1 9 HELIX 53 53 ALA F 52 LYS F 55 5 4 HELIX 54 54 PHE F 59 THR F 68 1 10 HELIX 55 55 ASN F 81 GLY F 91 1 11 HELIX 56 56 ASN F 94 ALA F 98 5 5 HELIX 57 57 THR F 102 ALA F 108 1 7 HELIX 58 58 SER F 121 PHE F 133 1 13 HELIX 59 59 ALA F 134 ILE F 138 5 5 HELIX 60 60 LYS G 11 LYS G 17 1 7 HELIX 61 61 VAL G 19 ALA G 30 1 12 HELIX 62 62 SER G 43 TYR G 51 1 9 HELIX 63 63 ALA G 52 LYS G 55 5 4 HELIX 64 64 PHE G 59 THR G 68 1 10 HELIX 65 65 ASN G 81 GLY G 91 1 11 HELIX 66 66 ASN G 94 ALA G 98 5 5 HELIX 67 67 THR G 102 ALA G 108 1 7 HELIX 68 68 SER G 121 PHE G 133 1 13 HELIX 69 69 ALA G 134 ILE G 138 5 5 HELIX 70 70 LYS H 11 LYS H 17 1 7 HELIX 71 71 VAL H 19 ALA H 30 1 12 HELIX 72 72 SER H 43 TYR H 51 1 9 HELIX 73 73 ALA H 52 LYS H 55 5 4 HELIX 74 74 PHE H 60 MET H 67 1 8 HELIX 75 75 ASN H 81 GLY H 91 1 11 HELIX 76 76 THR H 102 ALA H 108 1 7 HELIX 77 77 SER H 121 PHE H 133 1 13 HELIX 78 78 ALA H 134 ILE H 138 5 5 SHEET 1 A 4 LYS A 33 LEU A 40 0 SHEET 2 A 4 VAL A 72 GLU A 80 -1 O GLU A 78 N LYS A 33 SHEET 3 A 4 THR A 3 ILE A 10 -1 N ILE A 10 O VAL A 73 SHEET 4 A 4 VAL A 116 GLY A 118 -1 O HIS A 117 N ILE A 9 SHEET 1 B 4 LYS B 33 LEU B 40 0 SHEET 2 B 4 VAL B 72 GLU B 80 -1 O VAL B 72 N LEU B 40 SHEET 3 B 4 THR B 3 ILE B 10 -1 N SER B 8 O GLN B 75 SHEET 4 B 4 VAL B 116 GLY B 118 -1 O HIS B 117 N ILE B 9 SHEET 1 C 4 LYS C 33 LEU C 40 0 SHEET 2 C 4 VAL C 72 GLU C 80 -1 O VAL C 76 N VAL C 35 SHEET 3 C 4 THR C 3 ILE C 10 -1 N ILE C 10 O VAL C 73 SHEET 4 C 4 VAL C 116 GLY C 118 -1 O HIS C 117 N ILE C 9 SHEET 1 D 4 LYS D 33 LEU D 40 0 SHEET 2 D 4 VAL D 72 GLU D 80 -1 O GLU D 78 N LYS D 33 SHEET 3 D 4 THR D 3 ILE D 10 -1 N SER D 8 O GLN D 75 SHEET 4 D 4 VAL D 116 GLY D 118 -1 O HIS D 117 N ILE D 9 SHEET 1 E 4 LYS E 33 LEU E 40 0 SHEET 2 E 4 VAL E 72 GLU E 80 -1 O GLU E 78 N LYS E 33 SHEET 3 E 4 THR E 3 ILE E 10 -1 N SER E 8 O GLN E 75 SHEET 4 E 4 VAL E 116 GLY E 118 -1 O HIS E 117 N ILE E 9 SHEET 1 F 4 LYS F 33 LEU F 40 0 SHEET 2 F 4 VAL F 72 GLU F 80 -1 O GLU F 78 N LYS F 33 SHEET 3 F 4 THR F 3 ILE F 10 -1 N SER F 8 O GLN F 75 SHEET 4 F 4 VAL F 116 GLY F 118 -1 O HIS F 117 N ILE F 9 SHEET 1 G 4 LYS G 33 LEU G 40 0 SHEET 2 G 4 VAL G 72 GLU G 80 -1 O VAL G 74 N LYS G 38 SHEET 3 G 4 THR G 3 ILE G 10 -1 N ILE G 10 O VAL G 73 SHEET 4 G 4 VAL G 116 GLY G 118 -1 O HIS G 117 N ILE G 9 SHEET 1 H 4 LYS H 33 GLN H 41 0 SHEET 2 H 4 PRO H 71 GLU H 80 -1 O GLU H 78 N LYS H 33 SHEET 3 H 4 THR H 3 ILE H 10 -1 N GLU H 4 O GLY H 79 SHEET 4 H 4 VAL H 116 GLY H 118 -1 O HIS H 117 N ILE H 9 CRYST1 186.489 93.149 68.410 90.00 103.60 90.00 C 1 2 1 32 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 0.005362 0.000000 0.001298 0.00000 SCALE2 0.000000 0.010735 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015040 0.00000