+Open data
-Basic information
Entry | Database: PDB / ID: 2uvk | ||||||
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Title | Structure of YjhT | ||||||
Components | YJHT | ||||||
Keywords | UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / SIALIC ACID METABOLISM / KELCH REPEAT / BETA-PROPELLER | ||||||
Function / homology | N-acetylneuraminate epimerase / Mutatrotase, YjhT-like / racemase and epimerase activity, acting on carbohydrates and derivatives / Kelch-type beta propeller / outer membrane-bounded periplasmic space / carbohydrate metabolic process / N-acetylneuraminate epimerase Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Muller, A. / Severi, E. / Wilson, K.S. / Thomas, G.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Sialic Acid Mutarotation is Catalyzed by the Escherichia Coli Beta-Propeller Protein Yjht. Authors: Severi, E. / Muller, A. / Potts, J.R. / Leech, A. / Williamson, D. / Wilson, K.S. / Thomas, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uvk.cif.gz | 289.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uvk.ent.gz | 246 KB | Display | PDB format |
PDBx/mmJSON format | 2uvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uvk_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 2uvk_full_validation.pdf.gz | 434.1 KB | Display | |
Data in XML | 2uvk_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 2uvk_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uvk ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uvk | HTTPS FTP |
-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: 38872.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P39371 #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: 2.06 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 150 NL OF SEMET-SUBSTITUTED YJHT AND 150 NL OF 200 MM SODIUM MALONATE, 0.1M BIS TRIS PROPANE PH 7.5 AND 20% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→52.85 Å / Num. obs: 107873 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.9 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.5→73.13 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.403 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→73.13 Å
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Refine LS restraints |
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