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Yorodumi- PDB-2cy0: Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cy0 | ||||||
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Title | Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP | ||||||
Components | shikimate 5-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Shikimate / Cofactor / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structures of Shikimate Dehydrogenase AroE from Thermus thermophilus HB8 and its Cofactor and Substrate Complexes: Insights into the Enzymatic Mechanism Authors: Bagautdinov, B. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cy0.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cy0.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cy0_validation.pdf.gz | 755.4 KB | Display | wwPDB validaton report |
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Full document | 2cy0_full_validation.pdf.gz | 771.1 KB | Display | |
Data in XML | 2cy0_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 2cy0_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/2cy0 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/2cy0 | HTTPS FTP |
-Related structure data
Related structure data | 1wxdSC 2d5cC 2ev9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28316.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: AroE / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SJF8, shikimate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | ChemComp-NAP / | #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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 Details: Ammonium sulfate, Sodium Acetate trihydrate, PEG4000, pH 4.6, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2005 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.15 Å / Num. all: 39339 / Num. obs: 39285 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3487 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WXD Resolution: 1.9→31.15 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→31.15 Å
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Refine LS restraints |
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