+Open data
-Basic information
Entry | Database: PDB / ID: 4klk | ||||||
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Title | Phage-related protein DUF2815 from Enterococcus faecalis | ||||||
Components | Phage-related protein DUF2815 | ||||||
Keywords | UNKNOWN FUNCTION / structural genomics / phage-related protein / DUF2815 / pfam10991 / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Enterobacter phage Enc34, ssDNA-binding protein / Enterobacter phage Enc34, ssDNA-binding protein / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / ETHANOL / Uncharacterized protein Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å | ||||||
Authors | Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Phage-related protein DUF2815 from Enterococcus faecalis Authors: Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4klk.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4klk.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 4klk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4klk_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 4klk_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 4klk_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 4klk_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/4klk ftp://data.pdbj.org/pub/pdb/validation_reports/kl/4klk | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20098.926 Da / Num. of mol.: 1 / Fragment: UNP residues 4-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0322 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q838W1 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-EOH / |
#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: 2.73 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Tris buffer, 15% ethanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→36.6 Å / Num. all: 18291 / Num. obs: 18291 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.096 / Χ2: 4.645 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.93→36.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 11.226 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 146.75 Å2 / Biso mean: 59.7512 Å2 / Biso min: 31.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→36.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.928→1.978 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.0239 Å / Origin y: 58.5566 Å / Origin z: 15.959 Å
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