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Yorodumi- PDB-2au5: Structure of a conserved domain from locus EF2947 from Enterococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2au5 | ||||||
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Title | Structure of a conserved domain from locus EF2947 from Enterococcus faecalis V583 | ||||||
Components | conserved domain protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | EF2947-like / Protein of unknown function DUF3206 / EF2947-like superfamily / Protein of unknown function (DUF3206) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Cuff, M.E. / Moy, S. / Mulligan, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of a conserved domain from locus EF2947 from Enterococcus faecalis V583 Authors: Cuff, M.E. / Moy, S. / Mulligan, R. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2au5.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2au5.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 2au5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2au5_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 2au5_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 2au5_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 2au5_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/2au5 ftp://data.pdbj.org/pub/pdb/validation_reports/au/2au5 | 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: 16224.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF2947 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q82ZV0 |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.1 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 1K, imidazole, calcium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956, 0.97973 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2005 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→43 Å / Num. all: 7557 / Num. obs: 7557 / % possible obs: 97.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||
Reflection shell | Resolution: 2.1→2.155 Å / % possible all: 99.66 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→35.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.885 / SU B: 11.386 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.283 / ESU R Free: 0.248 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 46.885 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→35.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.9109 Å / Origin y: 16.0003 Å / Origin z: 9.4113 Å
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