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- PDB-3n8n: Crystal structure of 3-dehydroquinate dehydratase from Mycobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n8n | ||||||
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Title | Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 6 | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | LYASE/LYASE INHIBITOR / dehydroquinate dehydratase / aroD / Mycobacterium tuberculosis / shikimate pathway / drug discovery / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 647.2 KB | Display | ![]() |
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PDB format | ![]() | 534.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3n59C ![]() 3n76C ![]() 3n7aSC ![]() 3n86C ![]() 3n87C ![]() 3n8kC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15807.932 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase #2: Chemical | ChemComp-N88 / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 298 K / Method: microbath on oil / pH: 7.5 Details: potassium bromate Peg 2000mme, pH 7.5, microbath on oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: 2009 / Details: mirrors |
Radiation | Monochromator: Si (311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→62.3 Å / Num. all: 133469 / Num. obs: 115676 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.3 / Num. unique all: 16264 / % possible all: 84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3N7A Resolution: 2.5→62.3 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.841 / SU B: 12.037 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.389 / 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: 33.898 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→62.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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