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Yorodumi- PDB-2egz: Crystal structure of the 3-dehydroquinate dehydratase from Aquife... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2egz | ||||||
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Title | Crystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5 | ||||||
Components | 3-dehydroquinate dehydratase | ||||||
Keywords | LYASE / 3-dehydroquinate dehydratase / Aquifex aeolicus VF5 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Karthe, P. / Kumarevel, T.S. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the 3-dehydroquinate dehydratase from Aquifex aeolicus VF5 Authors: Karthe, P. / Kumarevel, T.S. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2egz.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2egz.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2egz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/2egz ftp://data.pdbj.org/pub/pdb/validation_reports/eg/2egz | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 25004.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aroD / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O66440, 3-dehydroquinate dehydratase #2: Chemical | #3: 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: 2.13 Å3/Da / Density % sol: 42.18 % / Description: the file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: liquid diffusion / pH: 5.6 Details: 30% PEG 4000, 0.2M Ammonium acetate, 0.1M Citrate pH5.6, LIQUID DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 180 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788, 0.900, 0.9794 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 15, 2006 | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→50 Å / Num. obs: 80554 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.08 | ||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.287 / Num. unique all: 3944 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→19.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 123083.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.75 Å2 / ksol: 0.404824 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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