HEADER DNA BINDING PROTEIN 04-MAR-97 1AE3 TITLE MUTANT R82C OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENE V PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: GEN V IN BACTERIOPHAGE F1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: K561; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTT18; SOURCE 10 EXPRESSION_SYSTEM_GENE: GENE V KEYWDS MUTANT, R82C, GVP, SINGLE-STRANDED DNA BINDING PROTEIN, DNA KEYWDS 2 REPLICATION, DNA-BINDING PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SU,Y.-G.GAO,H.ZHANG,T.C.TERWILLIGER,A.H.-J.WANG REVDAT 5 07-FEB-24 1AE3 1 REMARK REVDAT 4 03-NOV-21 1AE3 1 KEYWDS SEQADV REVDAT 3 13-JUL-11 1AE3 1 VERSN REVDAT 2 24-FEB-09 1AE3 1 VERSN REVDAT 1 04-SEP-97 1AE3 0 JRNL AUTH S.SU,Y.G.GAO,H.ZHANG,T.C.TERWILLIGER,A.H.WANG JRNL TITL ANALYSES OF THE STABILITY AND FUNCTION OF THREE SURFACE JRNL TITL 2 MUTANTS (R82C, K69H, AND L32R) OF THE GENE V PROTEIN FROM FF JRNL TITL 3 PHAGE BY X-RAY CRYSTALLOGRAPHY. JRNL REF PROTEIN SCI. V. 6 771 1997 JRNL REFN ISSN 0961-8368 JRNL PMID 9098886 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 58.8 REMARK 3 NUMBER OF REFLECTIONS : 4758 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 SET) : 0.181 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 498 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 387 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 46 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.043 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.61330 REMARK 3 B22 (A**2) : -1.44160 REMARK 3 B33 (A**2) : -0.17170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.52830 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 3.450 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.540 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.380 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.780 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19XM.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO) REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-96 REMARK 200 TEMPERATURE (KELVIN) : 285 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS IIC REMARK 200 DATA SCALING SOFTWARE : R-AXIS II REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4758 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIERS REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: R82C GVP WAS CRYSTALLIZED FROM REMARK 280 SOLUTIONS CONTAINING 10 MG/ML PROTEIN, 35 MM TRIS (PH7.0), AND REMARK 280 4.7% PEG 4000 (W/V), EQUILIBRATED AGAINST 6% PEG 4000. 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 38.57000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.57000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.97000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 HH TYR A 56 H1 HOH A 91 0.92 REMARK 500 H LEU A 60 H1 HOH A 95 1.06 REMARK 500 HG SER A 20 H LYS A 24 1.24 REMARK 500 HG SER A 67 H CYS A 82 1.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HZ1 LYS A 24 H2 HOH A 122 1545 1.04 REMARK 500 HH11 ARG A 80 H2 HOH A 128 4545 1.08 REMARK 500 H1 HOH A 119 H1 HOH A 132 1565 1.12 REMARK 500 HE21 GLN A 22 H2 HOH A 105 4545 1.31 REMARK 500 HH11 ARG A 16 H1 HOH A 117 1545 1.32 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 ARG A 16 CB - CG - CD ANGL. DEV. = -16.4 DEGREES REMARK 500 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 16 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 LEU A 28 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.3 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 GLN A 22 50.55 -90.01 REMARK 500 ASP A 79 -71.12 -79.32 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AE3 A 1 86 UNP P69543 VHED_BPF1 1 86 SEQADV 1AE3 CYS A 82 UNP P69543 ARG 82 ENGINEERED MUTATION SEQRES 1 A 86 MET ILE LYS VAL GLU ILE LYS PRO SER GLN ALA GLN PHE SEQRES 2 A 86 THR THR ARG SER GLY VAL SER ARG GLN GLY LYS PRO TYR SEQRES 3 A 86 SER LEU ASN GLU GLN LEU CYS TYR VAL ASP LEU GLY ASN SEQRES 4 A 86 GLU TYR PRO VAL LEU VAL LYS ILE THR LEU ASP GLU GLY SEQRES 5 A 86 GLN PRO ALA TYR ALA PRO GLY LEU TYR THR VAL HIS LEU SEQRES 6 A 86 SER SER PHE LYS VAL GLY GLN PHE GLY SER LEU MET ILE SEQRES 7 A 86 ASP ARG LEU CYS LEU VAL PRO ALA FORMUL 2 HOH *47(H2 O) HELIX 1 1 PRO A 8 GLN A 10 5 3 HELIX 2 2 LEU A 65 SER A 67 5 3 SHEET 1 A 3 LYS A 3 ILE A 6 0 SHEET 2 A 3 GLY A 59 VAL A 63 -1 N TYR A 61 O VAL A 4 SHEET 3 A 3 LEU A 83 PRO A 85 -1 N VAL A 84 O THR A 62 SHEET 1 B 3 THR A 14 VAL A 19 0 SHEET 2 B 3 PRO A 25 VAL A 35 -1 N GLU A 30 O THR A 14 SHEET 3 B 3 VAL A 43 THR A 48 -1 N ILE A 47 O GLN A 31 SHEET 1 C 2 PHE A 68 VAL A 70 0 SHEET 2 C 2 LEU A 76 ILE A 78 -1 N MET A 77 O LYS A 69 CRYST1 77.140 27.940 42.190 90.00 102.50 90.00 C 1 2 1 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 0.012963 0.000000 0.002874 0.00000 SCALE2 0.000000 0.035791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024278 0.00000