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Yorodumi- PDB-2ysw: Crystal Structure of the 3-dehydroquinate dehydratase from Aquife... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ysw | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Tanaka, T. / Kumarevel, T.S. / Ebihara, A. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / 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: Kumarevel, T.S. / Tanaka, T. / 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 | 2ysw.cif.gz | 143.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ysw.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ysw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/2ysw ftp://data.pdbj.org/pub/pdb/validation_reports/ys/2ysw | HTTPS FTP |
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-Related structure data
Related structure data | 2egzS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 25004.783 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O66440, 3-dehydroquinate dehydratase #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: 3.13 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 291 K / Method: liquid diffusion / pH: 4.8 Details: 44% MPD, 0.1M Acetate NaOH, 0.05M Magnesium chloride, pH 4.80, LIQUID DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 45453 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 26.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.318 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EGZ Resolution: 2.25→19.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4015365.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.12 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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