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- PDB-1pfs: SOLUTION NMR STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 1pfs
TitleSOLUTION NMR STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN OF THE FILAMENTOUS PSEUDOMONAS PHAGE PF3, MINIMIZED AVERAGE STRUCTURE
ComponentsPF3 SINGLE-STRANDED DNA BINDING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / VIRAL / BACTERIOPHAGE PF3 / SINGLE-STRANDED DNA
Function / homology
Function and homology information


DNA replication / DNA binding
Similarity search - Function
Single-stranded DNA-binding protein, Pseudomonas / Phage single-stranded DNA-binding protein / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA-Binding protein G5P
Similarity search - Component
Biological speciesPseudomonas phage Pf3 (virus)
MethodSOLUTION NMR
AuthorsFolmer, R.H.A. / Nilges, M. / Konings, R.N.H. / Hilbers, C.W.
Citation
Journal: EMBO J. / Year: 1995
Title: Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.
Authors: Folmer, R.H. / Nilges, M. / Konings, R.N. / Hilbers, C.W.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: Secondary Structure of the Single-Stranded DNA Binding Protein Encoded by Filamentous Phage Pf3 as Determined by NMR
Authors: Folmer, R.H. / Folkers, P.J. / Kaan, A. / Jonker, A.J. / Aelen, J.M. / Konings, R.N. / Hilbers, C.W.
#2: Journal: J.Virol. / Year: 1985
Title: Nucleotide Sequence of the Genome of Pf3, an Inc(P)-1 Plasmid-Specific Filamentous Bacteriophage of Pseudomonas Aeruginosa
Authors: Luiten, R.G. / Putterman, D.G. / Schoenmakers, J.G. / Konings, R.N. / Day, L.A.
History
DepositionAug 3, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: pdbx_database_status / pdbx_nmr_spectrometer ...pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_database_status.process_site / _pdbx_nmr_spectrometer.manufacturer ..._pdbx_database_status.process_site / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct_keywords.text
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PF3 SINGLE-STRANDED DNA BINDING PROTEIN
B: PF3 SINGLE-STRANDED DNA BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,8062
Polymers17,8062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1830 Å2
ΔGint-14 kcal/mol
Surface area9910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 80OVERALL ENERGY
Representative

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Components

#1: Protein PF3 SINGLE-STRANDED DNA BINDING PROTEIN / PF3 SSDBP


Mass: 8903.060 Da / Num. of mol.: 2 / Mutation: F36H
Source method: isolated from a genetically manipulated source
Details: DIMERIC / Source: (gene. exp.) Pseudomonas phage Pf3 (virus) / Genus: Inovirus / Plasmid: PPF3VF36H / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: P03672

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C- AND 15N-EDITED 3D NOESY
121HMQC-J
131HAHB
141HACAHB-COSY
151HNHB
16113C
17115N SPIN-ECHO HSQC

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Sample preparation

Sample conditionspH: 4.4 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: 30 STRUCTURES WERE CALCULATED USING THE GEOMETRIC FORCE FIELD 'PARALLDHG.PRO'. THESE WERE SUBSEQUENTLY REFINED IN A 7 ANGSTROM SHELL OF WATER MOLECULES USING THE OPLS FORCE FIELD (TOPOPLSXX. ...Details: 30 STRUCTURES WERE CALCULATED USING THE GEOMETRIC FORCE FIELD 'PARALLDHG.PRO'. THESE WERE SUBSEQUENTLY REFINED IN A 7 ANGSTROM SHELL OF WATER MOLECULES USING THE OPLS FORCE FIELD (TOPOPLSXX.PRO) AND AVERAGED. THIS AVERAGED STRUCTURE WAS ENERGY MINIMIZED USING AGAIN 'PARALLDHG.PRO'. THE PROGRAM WAS MODIFIED TO USE FLOATING CHIRALITY. CHIRAL-CENTER RESTRAINT (A**3) : 0.352
NMR ensembleConformer selection criteria: OVERALL ENERGY / Conformers calculated total number: 80 / Conformers submitted total number: 1

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