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- PDB-3n59: Type II dehydroquinase from Mycobacterium Tuberculosis complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n59 | ||||||
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Title | Type II dehydroquinase from Mycobacterium Tuberculosis complexed with 3-dehydroshikimate | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | LYASE / DEHYDRATASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / tuberculosis / drug target / 3-dehydroshikimate / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Snee, W.C. / Palaninathan, S.K. / Sacchettini, J.C. / Dias, M.V.B. / Bromfield, K.M. / Payne, R. / Ciulli, A. / Howard, N.I. / Abell, C. / Blundell, T.L. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() 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 | ![]() | 644 KB | Display | ![]() |
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PDB format | ![]() | 522.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 669 KB | Display | ![]() |
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Full document | ![]() | 685.3 KB | Display | |
Data in XML | ![]() | 123.6 KB | Display | |
Data in CIF | ![]() | 173.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n76C ![]() 3n7aC ![]() 3n86C ![]() 3n87C ![]() 3n8kC ![]() 3n8nC ![]() 2dhqS S: Starting model for refinement C: citing same article ( |
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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: 18649.947 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-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 290 K / Method: microbatch Details: MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 ...Details: MtDHQase protein was concentrated to 10-15 mg/mL prior to crystallization, using Amicon Ultra MWCO 5 KDa protein concentrators. MtDHQase crystals were grown in 4 uL drops composed of 5-7 mg/mL protein incubated with 1.5-fold M excess of ligand, 15% PEG monomethyl ether 2,000, 0.075 M KBr, 25 mM Tris, 50 mM NaCl, 0.5 mM DTT, 0.5 mM EDTA, pH 7.5 in microbatch plates covered with 5 mL Als oil, Microbatch, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→50 Å / Num. all: 124512 / Num. obs: 124512 / % possible obs: 95.11 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2dhq Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.382 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.732 / ESU R Free: 0.304 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.126 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.58 Å / Total num. of bins used: 20
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