+Open data
-Basic information
Entry | Database: PDB / ID: 5odj | ||||||
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Title | Single-stranded DNA-binding protein from bacteriophage Enc34 | ||||||
Components | Single-stranded DNA-binding protein | ||||||
Keywords | DNA BINDING PROTEIN / DNA replication / DUF2815 / SSB / OB fold | ||||||
Function / homology | Enterobacter phage Enc34, ssDNA-binding protein / Enterobacter phage Enc34, ssDNA-binding protein / Nucleic acid-binding, OB-fold / DNA binding / metal ion binding / SsDNA-binding protein Function and homology information | ||||||
Biological species | Enterobacter phage Enc34 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Cernooka, E. / Rumnieks, J. / Kazaks, A. / Tars, K. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34. Authors: Cernooka, E. / Rumnieks, J. / Tars, K. / Kazaks, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5odj.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5odj.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 5odj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5odj_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
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Full document | 5odj_full_validation.pdf.gz | 419.6 KB | Display | |
Data in XML | 5odj_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 5odj_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/5odj ftp://data.pdbj.org/pub/pdb/validation_reports/od/5odj | 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: 22888.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter phage Enc34 (virus) / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6WYG2 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-tris methane, 0.3 M MgCl2, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97671 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97671 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.78 Å / Num. obs: 32072 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.062 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4638 / CC1/2: 0.579 / Rpim(I) all: 0.464 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 1.5→30.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.687 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50.58 Å
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