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Yorodumi- PDB-3phh: Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3phh | ||||||
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Title | Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate | ||||||
Components | Shikimate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / shikimate dehydrogenase / shikimate pathway / Helicobacter pylori / alpha/beta domain / Rossmann fold | ||||||
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: 1.42 Å | ||||||
Authors | Cheng, W.C. / Lin, S.C. / Wang, W.C. | ||||||
Citation | Journal: To be Published Title: Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate Authors: Cheng, W.C. / Lin, S.C. / 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 | 3phh.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phh.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 3phh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3phh_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 3phh_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 3phh_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3phh_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phh ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phh | 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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Unit cell |
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-Components
#1: Protein | Mass: 30138.961 Da / Num. of mol.: 1 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+) |
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#2: Chemical | ChemComp-SKM / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% PEG 8000, 0.1M BIS-TRIS, pH 5.5, 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 315r / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→30 Å / Num. obs: 47067 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.42→1.47 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4566 / Rsym value: 0.467 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PHG Resolution: 1.42→24.85 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R Free: 0.077 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.421→1.458 Å / Total num. of bins used: 20
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