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Yorodumi- PDB-3kux: Structure of the YPO2259 putative oxidoreductase from Yersinia pestis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kux | ||||||
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Title | Structure of the YPO2259 putative oxidoreductase from Yersinia pestis | ||||||
Components | Putative oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / oxidoreductase family / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Anderson, S.M. / Wawrzak, Z. / Gordon, E. / Kwon, K. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Structure of the YPO2259 putative oxidoreductase from Yersinia pestis Authors: Anderson, S.M. / Wawrzak, Z. / Gordon, E. / Kwon, K. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kux.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kux.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/3kux ftp://data.pdbj.org/pub/pdb/validation_reports/ku/3kux | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38719.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: mviM4, y2101, YPO2259, YP_2055 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q7CIK0, UniProt: A0A3N4BF22*PLUS |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 35% Tacsimate, 10mM magnesium chloride, 100mM HEPES, 300mM NDSB-195, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2009 / Details: beryllium lens |
Radiation | Monochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 13362 / Num. obs: 13282 / % possible obs: 99.4 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 3.2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.098 / Χ2: 0.988 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1267 / Χ2: 1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.75→46.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 25.893 / SU ML: 0.233 / SU R Cruickshank DPI: 0.735 / SU Rfree: 0.268 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.2 / ESU R: 0.73 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
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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: 99.2 Å2 / Biso mean: 22.948 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→46.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.816 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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