HEADER DNA BINDING PROTEIN 03-AUG-96 1PFS TITLE SOLUTION NMR STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN OF TITLE 2 THE FILAMENTOUS PSEUDOMONAS PHAGE PF3, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PF3 SINGLE-STRANDED DNA BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PF3 SSDBP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: DIMERIC SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE PF3; SOURCE 3 ORGANISM_TAXID: 10872; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: MC4100; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PPF3VF36H KEYWDS DNA-BINDING PROTEIN, VIRAL, BACTERIOPHAGE PF3, SINGLE-STRANDED DNA, KEYWDS 2 DNA BINDING PROTEIN EXPDTA SOLUTION NMR AUTHOR R.H.A.FOLMER,M.NILGES,R.N.H.KONINGS,C.W.HILBERS REVDAT 5 01-MAY-24 1PFS 1 REMARK REVDAT 4 06-NOV-19 1PFS 1 KEYWDS REMARK REVDAT 3 24-FEB-09 1PFS 1 VERSN REVDAT 2 01-APR-03 1PFS 1 JRNL REVDAT 1 12-FEB-97 1PFS 0 JRNL AUTH R.H.FOLMER,M.NILGES,R.N.KONINGS,C.W.HILBERS JRNL TITL SOLUTION STRUCTURE OF THE SINGLE-STRANDED DNA BINDING JRNL TITL 2 PROTEIN OF THE FILAMENTOUS PSEUDOMONAS PHAGE PF3: SIMILARITY JRNL TITL 3 TO OTHER PROTEINS BINDING TO SINGLE-STRANDED NUCLEIC ACIDS. JRNL REF EMBO J. V. 14 4132 1995 JRNL REFN ISSN 0261-4189 JRNL PMID 7556054 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.H.FOLMER,P.J.FOLKERS,A.KAAN,A.J.JONKER,J.M.AELEN, REMARK 1 AUTH 2 R.N.KONINGS,C.W.HILBERS REMARK 1 TITL SECONDARY STRUCTURE OF THE SINGLE-STRANDED DNA BINDING REMARK 1 TITL 2 PROTEIN ENCODED BY FILAMENTOUS PHAGE PF3 AS DETERMINED BY REMARK 1 TITL 3 NMR REMARK 1 REF EUR.J.BIOCHEM. V. 224 663 1994 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.G.LUITEN,D.G.PUTTERMAN,J.G.SCHOENMAKERS,R.N.KONINGS, REMARK 1 AUTH 2 L.A.DAY REMARK 1 TITL NUCLEOTIDE SEQUENCE OF THE GENOME OF PF3, AN INC(P)-1 REMARK 1 TITL 2 PLASMID-SPECIFIC FILAMENTOUS BACTERIOPHAGE OF PSEUDOMONAS REMARK 1 TITL 3 AERUGINOSA REMARK 1 REF J.VIROL. V. 56 268 1985 REMARK 1 REFN ISSN 0022-538X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 30 STRUCTURES WERE CALCULATED USING THE REMARK 3 GEOMETRIC FORCE FIELD 'PARALLDHG.PRO'. THESE WERE SUBSEQUENTLY REMARK 3 REFINED IN A 7 ANGSTROM SHELL OF WATER MOLECULES USING THE OPLS REMARK 3 FORCE FIELD (TOPOPLSXX.PRO) AND AVERAGED. THIS AVERAGED REMARK 3 STRUCTURE WAS ENERGY MINIMIZED USING AGAIN 'PARALLDHG.PRO'. THE REMARK 3 PROGRAM WAS MODIFIED TO USE FLOATING CHIRALITY. CHIRAL-CENTER REMARK 3 RESTRAINT (A**3) : 0.352 REMARK 4 REMARK 4 1PFS 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_1000175648. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 4.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C- AND 15N-EDITED 3D NOESY; REMARK 210 HMQC-J; HAHB; HACAHB-COSY; HNHB; REMARK 210 15N SPIN-ECHO HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : OVERALL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 THR B 6 H PHE B 28 1.54 REMARK 500 O THR A 6 H PHE A 28 1.54 REMARK 500 O ASN A 60 H GLU A 67 1.58 REMARK 500 O ASN B 60 H GLU B 67 1.58 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 ASN A 63 24.40 49.08 REMARK 500 ASN B 63 24.42 49.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 12 0.31 SIDE CHAIN REMARK 500 ARG A 58 0.29 SIDE CHAIN REMARK 500 ARG A 77 0.30 SIDE CHAIN REMARK 500 ARG B 12 0.31 SIDE CHAIN REMARK 500 ARG B 58 0.28 SIDE CHAIN REMARK 500 ARG B 77 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1PFS A 1 78 UNP P03672 VHED_BPPF3 1 78 DBREF 1PFS B 1 78 UNP P03672 VHED_BPPF3 1 78 SEQRES 1 A 78 MET ASN ILE GLN ILE THR PHE THR ASP SER VAL ARG GLN SEQRES 2 A 78 GLY THR SER ALA LYS GLY ASN PRO TYR THR PHE GLN GLU SEQRES 3 A 78 GLY PHE LEU HIS LEU GLU ASP LYS PRO HIS PRO LEU GLN SEQRES 4 A 78 CYS GLN PHE PHE VAL GLU SER VAL ILE PRO ALA GLY SER SEQRES 5 A 78 TYR GLN VAL PRO TYR ARG ILE ASN VAL ASN ASN GLY ARG SEQRES 6 A 78 PRO GLU LEU ALA PHE ASP PHE LYS ALA MET LYS ARG ALA SEQRES 1 B 78 MET ASN ILE GLN ILE THR PHE THR ASP SER VAL ARG GLN SEQRES 2 B 78 GLY THR SER ALA LYS GLY ASN PRO TYR THR PHE GLN GLU SEQRES 3 B 78 GLY PHE LEU HIS LEU GLU ASP LYS PRO HIS PRO LEU GLN SEQRES 4 B 78 CYS GLN PHE PHE VAL GLU SER VAL ILE PRO ALA GLY SER SEQRES 5 B 78 TYR GLN VAL PRO TYR ARG ILE ASN VAL ASN ASN GLY ARG SEQRES 6 B 78 PRO GLU LEU ALA PHE ASP PHE LYS ALA MET LYS ARG ALA SHEET 1 A 5 LEU A 38 PHE A 43 0 SHEET 2 A 5 PHE A 24 LEU A 29 -1 N LEU A 29 O LEU A 38 SHEET 3 A 5 ASN A 2 PHE A 7 -1 N THR A 6 O PHE A 28 SHEET 4 A 5 GLY A 51 ASN A 62 -1 N VAL A 55 O ILE A 3 SHEET 5 A 5 LYS A 76 ARG A 77 -1 N LYS A 76 O GLN A 54 SHEET 1 B 2 VAL A 11 THR A 15 0 SHEET 2 B 2 PRO A 21 GLN A 25 -1 N PHE A 24 O ARG A 12 SHEET 1 C 2 TYR A 57 ASN A 62 0 SHEET 2 C 2 ARG A 65 ASP A 71 -1 O ARG A 65 N ASN A 62 SHEET 1 D 5 LEU B 38 PHE B 43 0 SHEET 2 D 5 PHE B 24 LEU B 29 -1 N LEU B 29 O LEU B 38 SHEET 3 D 5 ASN B 2 PHE B 7 -1 N THR B 6 O PHE B 28 SHEET 4 D 5 GLY B 51 ASN B 62 -1 N VAL B 55 O ILE B 3 SHEET 5 D 5 LYS B 76 ARG B 77 -1 N LYS B 76 O GLN B 54 SHEET 1 E 2 VAL B 11 THR B 15 0 SHEET 2 E 2 PRO B 21 GLN B 25 -1 N PHE B 24 O ARG B 12 SHEET 1 F 2 TYR B 57 ASN B 62 0 SHEET 2 F 2 ARG B 65 ASP B 71 -1 O ARG B 65 N ASN B 62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000