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Yorodumi- PDB-1qvc: CRYSTAL STRUCTURE ANALYSIS OF SINGLE STRANDED DNA BINDING PROTEIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qvc | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF SINGLE STRANDED DNA BINDING PROTEIN (SSB) FROM E.COLI | ||||||
Components | SINGLE STRANDED DNA BINDING PROTEIN MONOMER | ||||||
Keywords | DNA BINDING PROTEIN / BETA-BARREL / SINGLE STRANDED DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information single-stranded DNA-binding protein complex / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding ...single-stranded DNA-binding protein complex / nucleoid / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Matsumoto, T. / Morimoto, Y. / Shibata, N. / Shimamoto, N. / Tsukihara, T. / Yasuoka, N. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2000 Title: Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis. Authors: Matsumoto, T. / Morimoto, Y. / Shibata, N. / Kinebuchi, T. / Shimamoto, N. / Tsukihara, T. / Yasuoka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qvc.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qvc.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qvc_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 1qvc_full_validation.pdf.gz | 499.2 KB | Display | |
Data in XML | 1qvc_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 1qvc_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qvc ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qvc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15472.161 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P02339, UniProt: P0AGE0*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: small tubes / pH: 9 Details: SODIUM CHLORIDE, AMMONIUM SULFATE, pH 9.0, SMALL TUBES, temperature 288K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4, 20 ℃ / Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→52 Å / Num. all: 150790 / Num. obs: 24956 / % possible obs: 82.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 39.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8 | ||||||||||||||||||||
Reflection shell | Resolution: 2.2→2.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.197 / % possible all: 43.5 | ||||||||||||||||||||
Reflection | *PLUS Num. measured all: 150790 | ||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 43.5 % |
-Processing
Software |
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Refinement | Resolution: 2.2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH, R. A. AND HUBER, R.
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 24884 / Rfactor Rwork: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 66.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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