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Yorodumi- PDB-2hta: Crystal Structure of a putative mutarotase (YeaD) from Salmonella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hta | ||||||
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Title | Crystal Structure of a putative mutarotase (YeaD) from Salmonella typhimurium in orthorhombic form | ||||||
Components | Putative enzyme related to aldose 1-epimerase | ||||||
Keywords | ISOMERASE / Salmonella typhimurium / carbohydrate / aldose 1-epimerase / mutarotase / YeaD / GalM / sugar phosphate | ||||||
Function / homology | Function and homology information glucose-6-phosphate 1-epimerase / glucose-6-phosphate 1-epimerase activity / carbohydrate binding / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure of the putative mutarotase YeaD from Salmonella typhimurium: structural comparison with galactose mutarotases. Authors: Chittori, S. / Simanshu, D.K. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hta.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hta.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/2hta ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2hta | HTTPS FTP |
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-Related structure data
Related structure data | 2htbC 1jovS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34343.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: IFO12529 / Gene: yeaD / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS References: UniProt: Q8ZPV9, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 3.01 Å3/Da / Density % sol: 59.1 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5- 2M ammonium sulfate, 25mM magnesium formate, 0.1M Na cacodylate pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MAC Science DIP-2040 / Detector: IMAGE PLATE / Date: Mar 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 63880 / % possible obs: 0.959 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5886 / % possible all: 0.938 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JOV Resolution: 1.9→39.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.877 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.129 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.213 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.897→1.946 Å / Total num. of bins used: 20
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