+Open data
-Basic information
Entry | Database: PDB / ID: 2gbo | ||||||
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Title | Protein of Unknown Function EF2458 from Enterococcus faecalis | ||||||
Components | UPF0358 protein EF2458 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Uncharacterised protein family UPF0358 / Protein of unknown function (DUF1507) / SO2669-like / UPF0358 superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / UPF0358 protein EF_2458 Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Osipiuk, J. / Wu, R. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of conserved hypothetical protein EF_2458 from Enterococcus faecalis. Authors: Osipiuk, J. / Wu, R. / Bargassa, M. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gbo.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gbo.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gbo ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gbo | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12164.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2458 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q831P3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 35% (v/v) 2-methyl-2,4-pentanediol, 0.1 M HEPES, 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2006 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.4 Å / Num. all: 12040 / Num. obs: 12040 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.83 / Num. unique all: 933 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→39.5 Å / Cor.coef. Fo:Fc: 0.961 / SU B: 9.843 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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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: 53.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→39.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 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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