+Open data
-Basic information
Entry | Database: PDB / ID: 2ox1 | ||||||
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Title | Archaeal Dehydroquinase | ||||||
Components | 3-dehydroquinate dehydratase | ||||||
Keywords | LYASE / (beta-alpha)8 barrel | ||||||
Function / homology | Function and homology information 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.33 Å | ||||||
Authors | Gallagher, D.T. / Smith, N.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structure and lability of archaeal dehydroquinase. Authors: Smith, N.N. / Gallagher, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ox1.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ox1.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ox1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2ox1 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2ox1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological unit is a dimer. The crystal asymmetric unit contains two biological dimers. |
-Components
#1: Protein | Mass: 22237.307 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: aroD / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O30011, 3-dehydroquinate dehydratase #2: Chemical | ChemComp-GOL / #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: 2.91 Å3/Da / Density % sol: 57.68 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M ammonium acetate 0.1M sodium acetate 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2004 / Details: mirrors |
Radiation | Monochromator: mirror coating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→20 Å / Num. all: 43264 / Num. obs: 43264 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4 / Num. unique all: 4135 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.33→10 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.22 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.271 / 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: 30.226 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.33→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.387 Å / Total num. of bins used: 20
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