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Yorodumi- PDB-1d0i: CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COE... -
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-Basic information
Entry | Database: PDB / ID: 1d0i | ||||||
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Title | CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM STREPTOMYCES COELICOLOR COMPLEXED WITH PHOSPHATE IONS | ||||||
Components | TYPE II 3-DEHYDROQUINATE HYDRATASE | ||||||
Keywords | LYASE / TYPE II DEHYDROQUINASE / SHIKIMATE PATHWAY / DODECAMERIC QUATERNARY STRUCTURE / TETRAHEDRAL SYMMETRY | ||||||
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 | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Roszak, A.W. / Krell, T. / Hunter, I.S. / Coggins, J.R. / Lapthorn, A.J. | ||||||
Citation | 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 | 1d0i.cif.gz | 758.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d0i.ent.gz | 629.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d0i_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 1d0i_full_validation.pdf.gz | 497.7 KB | Display | |
Data in XML | 1d0i_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1d0i_validation.cif.gz | 70.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d0i ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d0i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16569.605 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Description: STREPTOMYCES COELICOLOR / Plasmid: PDHQ / Production host: Escherichia coli (E. coli) / References: UniProt: P15474, 3-dehydroquinate dehydratase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-TRS / #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: 2.74 Å3/Da / Density % sol: 55.15 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 8000, SODIUM/POTASSIUM PHOSPHATE, TRIS BUFFER, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 57.1 % | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.89 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.03 Å / Num. all: 199360 / Num. obs: 199360 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.82 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.593 / % possible all: 93.5 |
Reflection | *PLUS Num. measured all: 798417 |
Reflection shell | *PLUS % possible obs: 93.5 % |
-Processing
Software |
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Refinement | Resolution: 1.8→45.03 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: USED RESTRAINED REFINEMENT OF THE MAXIMUM LIKELIHOOD RESIDUAL WITH THE SPARSE MATRIX AND INDIVIDUAL ATOM ANISOTROPIC B FACTORS
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Refinement step | Cycle: LAST / Resolution: 1.8→45.03 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.2 % / Rfactor obs: 0.149 / Rfactor Rfree: 0.203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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