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Yorodumi- PDB-3phi: Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3phi | ||||||
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Title | Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate and NADPH | ||||||
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: 2.04 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 and NADPH 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 | 3phi.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phi.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 3phi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3phi_validation.pdf.gz | 989 KB | Display | wwPDB validaton report |
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Full document | 3phi_full_validation.pdf.gz | 1004.2 KB | Display | |
Data in XML | 3phi_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 3phi_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phi ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phi | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30138.961 Da / Num. of mol.: 2 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: Chemical | #3: Chemical | #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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% PEG 8000, 0.1M BIS-TRIS, pH 6.0, 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: 0.9762 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→30 Å / Num. obs: 32329 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 10.3 / Num. unique all: 2979 / Rsym value: 0.131 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PHG Resolution: 2.04→28.23 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / 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: 34.245 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→28.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.043→2.096 Å / Total num. of bins used: 20
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