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Yorodumi- PDB-1pfs: SOLUTION NMR STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN... -
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-Basic information
Entry | Database: PDB / ID: 1pfs | ||||||
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Title | SOLUTION NMR STRUCTURE OF THE SINGLE-STRANDED DNA BINDING PROTEIN OF THE FILAMENTOUS PSEUDOMONAS PHAGE PF3, MINIMIZED AVERAGE STRUCTURE | ||||||
Components | PF3 SINGLE-STRANDED DNA BINDING PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / VIRAL / BACTERIOPHAGE PF3 / SINGLE-STRANDED DNA | ||||||
Function / homology | Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / DNA replication / Nucleic acid-binding, OB-fold / Beta Barrel / DNA binding / Mainly Beta / DNA-Binding protein G5P Function and homology information | ||||||
Biological species | Pseudomonas phage Pf3 (virus) | ||||||
Method | SOLUTION NMR | ||||||
Authors | Folmer, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pfs.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pfs.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pfs_validation.pdf.gz | 338.6 KB | Display | wwPDB validaton report |
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Full document | 1pfs_full_validation.pdf.gz | 340.9 KB | Display | |
Data in XML | 1pfs_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1pfs_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/1pfs ftp://data.pdbj.org/pub/pdb/validation_reports/pf/1pfs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 4.4 / Temperature: 300 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software | Name: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement | ||||||||||||
Refinement | Software 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 ensemble | Conformer selection criteria: OVERALL ENERGY / Conformers calculated total number: 80 / Conformers submitted total number: 1 |