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Yorodumi- PDB-6hs9: The crystal structure of type II Dehydroquinase from Butyrivibrio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hs9 | ||||||
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Title | The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876 | ||||||
Components | 3-dehydroquinate dehydratase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / shikimate pathway / dehydratase | ||||||
Function / homology | Function and homology information quinate catabolic 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 | Butyrivibrio crossotus DSM 2876 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å | ||||||
Authors | Lapthorn, A.J. / Roszak, A.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876 Authors: Lapthorn, A.J. / Ner, L. / Roszak, A.W. #1: Journal: AMB Express / Year: 2015 Title: Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway. Authors: Liu, C. / Liu, Y.M. / Sun, Q.L. / Jiang, C.Y. / Liu, S.J. #2: Journal: Structure / Year: 2002 Title: The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor. Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hs9.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hs9.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 6hs9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hs9_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 6hs9_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 6hs9_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 6hs9_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/6hs9 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/6hs9 | HTTPS FTP |
-Related structure data
Related structure data | 6hs8C 6hsaC 6hsbC 6hsqC 1gqoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16387.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Butyrivibrio crossotus DSM 2876 (bacteria) Gene: aroQ, BUTYVIB_01550 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D4S0D1, 3-dehydroquinate dehydratase |
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#2: Chemical | ChemComp-3DS / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % / Description: hexagonal prism |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 8000, 0.1M CaCl2, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.82656 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→32.04 Å / Num. obs: 119959 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 12.298 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.028 / Rrim(I) all: 0.047 / Net I/σ(I): 13.9 / Num. measured all: 292996 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2186 / CC1/2: 0.477 / Rpim(I) all: 0.559 / Rrim(I) all: 0.914 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GQO Resolution: 1.05→32 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.72 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.02 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74 Å2 / Biso mean: 21.112 Å2 / Biso min: 8.76 Å2
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Refinement step | Cycle: final / Resolution: 1.05→32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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