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Yorodumi- PDB-2oeq: Protein of Unknown Function (DUF964) from Bacillus stearothermophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oeq | ||||||
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Title | Protein of Unknown Function (DUF964) from Bacillus stearothermophilus | ||||||
Components | Protein of unknown function, DUF964 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / helix bundle / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | YheA/YmcA-like / Control of competence regulator ComK, YlbF/YmcA / YheA/YmcA-like domain superfamily / Control of competence regulator ComK, YlbF/YmcA / YheA-like fold / Up-down Bundle / Mainly Alpha / UPF0342 protein GK0640 Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Kim, Y. / Wu, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Protein of Unknown Function from Bacillus stearothermophilus Authors: Kim, Y. / Wu, R. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT UNIPROT DATABASE AT THE TIME OF DEPOSITION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oeq.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oeq.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oeq_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 2oeq_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 2oeq_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2oeq_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/2oeq ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oeq | 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: 14541.435 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5L2A5*PLUS #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: 2.19 Å3/Da / Density % sol: 43.73 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.2M Potassium dihydrogen phosphate, 15% PEG3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97907, 0.97923 | |||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 2, 2003 / Details: mirrors | |||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→55.9 Å / Num. all: 10827 / Num. obs: 10827 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.25 % / Limit h max: 15 / Limit h min: -14 / Limit k max: 18 / Limit k min: -17 / Limit l max: 20 / Limit l min: 0 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.2 | |||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1085 / % possible all: 70.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→34.17 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.826 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.595 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.145 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→34.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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