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Yorodumi- PDB-2p0o: Crystal structure of a conserved protein from locus EF_2437 in En... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p0o | ||||||
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Title | Crystal structure of a conserved protein from locus EF_2437 in Enterococcus faecalis with an unknown function | ||||||
Components | Hypothetical protein DUF871Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / TIM barrel / PF05913 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Cuff, M.E. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The structure of a conserved protein from locus EF_2437 in Enterococcus faecalis with an unknown function. Authors: Cuff, M.E. / Zhou, M. / Moy, S. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. | ||||||
Remark 999 | SEQUENCE AUTHORS STATE THAT THE ELECTRON DENSITY SUGGESTS ASP, NOT GLU. GLU SIDECHAIN IS TOO BIG ... SEQUENCE AUTHORS STATE THAT THE ELECTRON DENSITY SUGGESTS ASP, NOT GLU. GLU SIDECHAIN IS TOO BIG TO FIT THE DENSITY. THE CODONS FOR THESE RESIDUES DIFFER ONLY IN THE 3RD BASE. THIS COULD BE EITHER A CLONING OR SEQUENCING ERROR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p0o.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p0o.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2p0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/2p0o ftp://data.pdbj.org/pub/pdb/validation_reports/p0/2p0o | HTTPS FTP |
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-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: 42370.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2437 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q831R3 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#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: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 25% PEG 3350, 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: 0.97935 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2006 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→33.9 Å / Num. all: 23984 / Num. obs: 23984 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 57.2 Å2 / Rsym value: 0.091 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.384 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→33.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.763 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.188 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: 57.231 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→33.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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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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