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Yorodumi- PDB-4fpx: Crystal Structure of Shikimate Dehydrogenase (aroE) Q237N Mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fpx | ||||||
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Title | Crystal Structure of Shikimate Dehydrogenase (aroE) Q237N Mutant from Helicobacter pylori | ||||||
Components | Shikimate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 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: 2.4 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 | 4fpx.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fpx.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fpx_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 4fpx_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 4fpx_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4fpx_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/4fpx ftp://data.pdbj.org/pub/pdb/validation_reports/fp/4fpx | HTTPS FTP |
-Related structure data
Related structure data | 3phgS 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: 30367.205 Da / Num. of mol.: 2 / Mutation: Q237N 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: 2.03 Å3/Da / Density % sol: 39.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M sodium acetate, 0.1M Tris, 36% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. obs: 18960 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Χ2: 1.073 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 3PHG Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.999 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.798 / ESU R Free: 0.283 / 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: 66.41 Å2 / Biso mean: 28.9081 Å2 / Biso min: 2.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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