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- PDB-4civ: Crystal structure of Mycobacterium tuberculosis type 2 dehydroqui... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4civ | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-hydroxymethylcyclohex-2-ene-1-carboxylic acid | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / BACTERIAL PROTEINS / INHIBITOR / PROTEIN BINDING / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Otero, J.M. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / Blanco, B. / Sedes, A. / Peon, A. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
![]() | ![]() Title: Exploring the water-binding pocket of the type II dehydroquinase enzyme in the structure-based design of inhibitors. Authors: Blanco, B. / Sedes, A. / Peon, A. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.6 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ciwC ![]() 4cixC ![]() 4ciyC ![]() 2y71S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 15676.737 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase |
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#2: Chemical | ChemComp-48P / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.8 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 32% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE-1-ETHANESULFONIC ACID SODIUM SALT (HEPES) PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012 / Details: PT COATED SI MIRROR |
Radiation | Monochromator: HORIZONTALLY DIFFRACTING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→38 Å / Num. obs: 3103 / % possible obs: 81.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y71 Resolution: 2.9→36.45 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 22.233 / SU ML: 0.394 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY GAP BY DISORDERED REGION BETWEEN ARG-19 AND GLY-25 INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY GAP BY DISORDERED REGION BETWEEN ARG-19 AND GLY-25 INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO- CRYSTALS IN INHIBITOR SOLUTION
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.937 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→36.45 Å
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Refine LS restraints |
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