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Yorodumi- PDB-5jbr: Crystal structure of uncharacterized protein Bcav_2135 from Beute... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jbr | ||||||
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Title | Crystal structure of uncharacterized protein Bcav_2135 from Beutenbergia cavernae | ||||||
Components | Uncharacterized protein Bcav_2135 | ||||||
Keywords | Structural Genomics / Unknown function / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Beutenbergia cavernae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Chang, C. / Cuff, M. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of uncharacterized protein Bcav_2135 from Beutenbergia cavernae Authors: Chang, C. / Cuff, M. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jbr.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jbr.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jbr ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jbr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16423.896 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: mutate M1V, A24T / Source: (gene. exp.) Beutenbergia cavernae (bacteria) / Strain: ATCC BAA-8 / DSM 12333 / NBRC 16432 / Gene: Bcav_2135 / Plasmid: pMCSG73 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C5C6I1 #2: Chemical | ChemComp-SO4 / #3: 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: 2.42 Å3/Da / Density % sol: 49.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: Lithium sulfate, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793149 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 17, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793149 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 36092 / % possible obs: 97.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.16 Å2 / Rmerge(I) obs: 0.041 / Net I/av σ(I): 29.24 / Net I/σ(I): 11.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→35.433 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.86 Å2 / Biso mean: 21.6258 Å2 / Biso min: 6.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→35.433 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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