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Yorodumi- PDB-3nhv: Crystal Structure of BH2092 protein from Bacillus halodurans, Nor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nhv | ||||||
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Title | Crystal Structure of BH2092 protein from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR228F | ||||||
Components | BH2092 protein | ||||||
Keywords | structural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published / Year: 2010 Title: Northeast Structural Genomics Consortium Target BhR228F Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nhv.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nhv.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/3nhv ftp://data.pdbj.org/pub/pdb/validation_reports/nh/3nhv | 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16449.406 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2092 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9KB42 #2: Chemical | ChemComp-CL / #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: 3.14 Å3/Da / Density % sol: 60.89 % |
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Crystal grow | Temperature: 291 K / Method: microbatch, under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M MES (pH 6), 40% PEG400, and 0.1M potassium chloride. , microbatch, under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97877 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97877 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→50 Å / Num. all: 75822 / Num. obs: 73851 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.061 / Net I/σ(I): 34.97 |
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5750 / Rsym value: 0.496 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→19.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 248247.578 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.081 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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