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Yorodumi- PDB-3khn: Crystal structure of putative MotB like protein DVU_2228 from Des... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3khn | ||||||
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Title | Crystal structure of putative MotB like protein DVU_2228 from Desulfovibrio vulgaris. | ||||||
Components | MotB protein, putative | ||||||
Keywords | structural genomics / unknown function / OmpA-like domain / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris str. Hildenborough (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å | ||||||
Authors | Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative MotB like protein DVU_2228 from Desulfovibrio vulgaris Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3khn.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3khn.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 3khn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/3khn ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3khn | 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: 19896.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria) Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Gene: DVU_2228 / Plasmid: pSGX4(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q729W9 #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: 1.91 Å3/Da / Density % sol: 35.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 30% PEG MME 550 0.05M Calcium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 20244 / Num. obs: 20244 / % possible obs: 98.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.052 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 22.4 / Num. unique all: 793 / Rsym value: 0.09 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.292 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.835 / SU B: 4.374 / SU ML: 0.123 / SU R Cruickshank DPI: 0.22 / SU Rfree: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 68.97 Å2 / Biso mean: 21.437 Å2 / Biso min: 6.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.033→2.086 Å / Total num. of bins used: 20
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