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Yorodumi- PDB-1h05: 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h05 | ||||||
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Title | 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SULPHATE | ||||||
Components | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
Keywords | DEHYDRATASE / SHIKIMATE PATHWAY / ALPHA/BETA PROTEIN / LYASE / AROMATIC AMINO ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Roszak, A.W. / Coggins, J.R. / Lapthorn, A.J. | ||||||
Citation | Journal: FEBS Lett. / Year: 2002 Title: Specificity of Substrate Recognition by Type II Dehydroquinases as Revealed by Binding of Polyanions(1) Authors: Evans, L. / Roszak, A.W. / Noble, L. / Robinson, D. / Chalk, P. / Matthews, J. / Coggins, J.R. / Price, N. / Lapthorn, A.J. #1: Journal: Nat.Struct.Biol. / Year: 1999 Title: The Two Types of 3-Dehydroquinase Have Different Structures But Catalyze the Same Overall Reaction Authors: Gourley, D.G. / Shrive, A.K. / Polikarpov, I. / Krell, T. / Coggins, J.R. / Hawkins, A.R. / Isaacs, N.W. / Sawyer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h05.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h05.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h05 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h05 | HTTPS FTP |
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-Related structure data
Related structure data | 2dhqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15676.737 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: MPET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P36918, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | CATALYZES TRANS-DEHYDRATIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.5 % Description: LOW COMPLETENESS AND REDUNDANCY IN HIGHEST RESOLUTION SHELL AS DATA WERE PROCESSED TO CORNERS OF CCD DETECTOR | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 30% MPD, 0.5M AMMONIUM SULPHATE 0.1M HEPES PH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
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: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 24274 / % possible obs: 89.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.832 / % possible all: 32.7 |
Reflection | *PLUS Highest resolution: 1.45 Å / Num. measured all: 85115 |
Reflection shell | *PLUS % possible obs: 32.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DHQ Resolution: 1.5→30 Å / σ(F): 0 / ESU R: 0.08894 / ESU R Free: 0.07971
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Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rwork: 0.1 / Num. reflection Rwork: 1141 / Total num. of bins used: 20 |