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Yorodumi- PDB-4foo: Crystal Structure of Shikimate Dehydrogenase (aroE) Q237K Mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4foo | ||||||
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Title | Crystal Structure of Shikimate Dehydrogenase (aroE) Q237K Mutant from Helicobacter pylori | ||||||
Components | Shikimate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / shikimate / dehydrogenase / NADP Binding | ||||||
Function / homology | Function and homology information shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Cheng, W.C. / Chen, T.J. / Wang, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4foo.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4foo.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 4foo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4foo_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 4foo_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 4foo_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 4foo_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/4foo ftp://data.pdbj.org/pub/pdb/validation_reports/fo/4foo | HTTPS FTP |
-Related structure data
Related structure data | 3phhS S: Starting model for refinement |
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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: 30382.283 Da / Num. of mol.: 2 / Mutation: Q237K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: aroE, HP_1249 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 References: UniProt: P56119, shikimate dehydrogenase (NADP+) #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: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M potassium acetate, 0.1M Tris, 23% PEG 3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Bent Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→30 Å / Num. obs: 16286 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.048 / Net I/σ(I): 10.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PHH Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.159 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.311 / 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: 62.6 Å2 / Biso mean: 26.2603 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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