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Yorodumi- PDB-3n76: Crystal structure of 3-dehydroquinate dehydratase from Mycobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n76 | ||||||
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Title | Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with compound 5 | ||||||
Components | 3-dehydroquinate dehydratase | ||||||
Keywords | LYASE/LYASE INHIBITOR / dehydroquinate dehydratase / aroD / shikimate pathway / drug discovery / mycobacterium tuberculosis / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
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: 1.9 Å | ||||||
Authors | Dias, M.V.B. / Snee, W.C. / Bromfield, K.M. / Payne, R. / Palaninathan, S.K. / Ciulli, A. / Howard, N.I. / Abell, C. / Sacchettini, J.C. / Blundell, T.L. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis. Authors: Dias, M.V. / Snee, W.C. / Bromfield, K.M. / Payne, R.J. / Palaninathan, S.K. / Ciulli, A. / Howard, N.I. / Abell, C. / Sacchettini, J.C. / Blundell, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n76.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n76.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n76_validation.pdf.gz | 716.7 KB | Display | wwPDB validaton report |
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Full document | 3n76_full_validation.pdf.gz | 718.9 KB | Display | |
Data in XML | 3n76_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3n76_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/3n76 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/3n76 | HTTPS FTP |
-Related structure data
Related structure data | 3n59C 3n7aC 3n86C 3n87C 3n8kC 3n8nC 1h0rS C: citing same article (ref.) S: Starting model for refinement |
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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: 15807.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroD, aroQ, MT2612, MTCY159.19, Rv2537c / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase |
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#2: Chemical | ChemComp-CA2 / ( |
#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: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Hepes, pH7.5 peg 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97825 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: 2009 Details: Si(111) monochromator. Mirror 1: Grazing angle 2.8 mrad, vertical focusing. Mir ror 2: vertical and horizontal focusing. |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97825 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.6 Å / Num. all: 13318 / Num. obs: 13302 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 17.725 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.121 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1 / Num. unique all: 1929 / Rsym value: 0.53 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H0R Resolution: 1.9→31.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.987 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.136 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.439 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.951 Å / Total num. of bins used: 20
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