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Yorodumi- PDB-4apv: The Klebsiella pneumoniae primosomal PriB protein: identification... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4apv | ||||||
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Title | The Klebsiella pneumoniae primosomal PriB protein: identification, crystal structure, and ssDNA binding mode | ||||||
Components | PRIMOSOMAL REPLICATION PROTEIN N | ||||||
Keywords | REPLICATION / PRIB PRIMOSOME SSDNA BINDING | ||||||
Function / homology | Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / : Function and homology information | ||||||
Biological species | KLEBSIELLA PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å | ||||||
Authors | Lo, Y.H. / Huang, Y.H. / Hsiao, C.D. / Huang, C.Y. | ||||||
Citation | Journal: Genes Cells / Year: 2012 Title: Crystal Structure and DNA-Binding Mode of Klebsiella Pneumoniae Primosomal Prib Protein. Authors: Huang, Y. / Lo, Y.H. / Huang, W. / Huang, C.Y. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4apv.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4apv.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 4apv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4apv_validation.pdf.gz | 426.6 KB | Display | wwPDB validaton report |
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Full document | 4apv_full_validation.pdf.gz | 428.2 KB | Display | |
Data in XML | 4apv_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 4apv_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/4apv ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4apv | HTTPS FTP |
-Related structure data
Related structure data | 1v1qS S: Starting model for refinement |
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Similar 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: 12559.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G0GH41 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.4 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 50% ETHANOL, 10 MM SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.4 Å / Num. obs: 5031 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 34.96 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 40.7 |
Reflection shell | Resolution: 2.09→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V1Q Resolution: 2.095→26.649 Å / SU ML: 0.3 / σ(F): 1.37 / Phase error: 28.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.888 Å2 / ksol: 0.389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.095→26.649 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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