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Yorodumi- PDB-2zbl: Functional annotation of Salmonella enterica yihS-encoded protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zbl | ||||||
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Title | Functional annotation of Salmonella enterica yihS-encoded protein | ||||||
Components | Putative isomerase | ||||||
Keywords | ISOMERASE / N-acyl-D-glucosamine 2-epimerase protein family | ||||||
Function / homology | Function and homology information sulfoquinovose isomerase / N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase Authors: Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zbl.cif.gz | 564.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zbl.ent.gz | 460.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zbl_validation.pdf.gz | 487.4 KB | Display | wwPDB validaton report |
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Full document | 2zbl_full_validation.pdf.gz | 511.1 KB | Display | |
Data in XML | 2zbl_validation.xml.gz | 114 KB | Display | |
Data in CIF | 2zbl_validation.cif.gz | 174.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zbl ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zbl | HTTPS FTP |
-Related structure data
Related structure data | 2rgkC 2afaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48589.516 Da / Num. of mol.: 6 / Mutation: H248A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: yihS / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS(174)DE3 / References: UniProt: Q8ZKT7 #2: Sugar | ChemComp-BMA / #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: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG10000, 0.1M Tris-HCl, pH8.0, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 297314 / % possible obs: 94.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.3 / Num. unique all: 27327 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AFA Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.518 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.087 / 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: 13.087 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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