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- PDB-2y76: Structure of Mycobacterium tuberculosis type II dehydroquinase co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y76 | ||||||
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Title | Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-3-(benzo(b)thiophen-5-ylmethoxy)-2-(benzo(b) thiophen-5-ylmethyl)-1,4,5-trihydroxycyclohex-2-enecarboxylate | ||||||
![]() | 3-DEHYDROQUINATE DEHYDRATASE | ||||||
![]() | LYASE / AMINO ACID BIOSYNTHESIS | ||||||
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. / Fox, G.C. / Tizon, L. / Prazeres, V.F.V. / Lamb, H. / Hawkins, A.R. / Ainsa, J.A. / Castedo, L. / Gonzalez-Bello, C. / van Raaij, M.J. | ||||||
![]() | ![]() Title: A prodrug approach for improving antituberculosis activity of potent Mycobacterium tuberculosis type II dehydroquinase inhibitors. Authors: Tizon, L. / Otero, J.M. / Prazeres, V.F. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Ainsa, J.A. / Castedo, L. / Gonzalez-Bello, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 42.8 KB | Display | ![]() |
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PDB format | ![]() | 30 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2y71C ![]() 2y77C ![]() 1h0sS 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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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-CB7 / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | INITIATOR METHIONINE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 33% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM EDTA, 200 MM SODIUM CHLORIDE 12.5 MM SODIUM ...Details: 33% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM EDTA, 200 MM SODIUM CHLORIDE 12.5 MM SODIUM (1R,4S,5R)- -3-(1-BENZOTHIOPHEN-5-YLMETHOXY)-2-(1-BENZOTHIOPHEN-5- YLMETHYL)-1,4,5-TRIHYDROXY-CYCLOHEX-2-ENE-1-CARBOXYLATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2010 Details: FOCUSING MIRRORS ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK- BAEZ GEOMETRY |
Radiation | Monochromator: HORIZONTALLY DIFFRACTING MONOCHROMATOR SI(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38 Å / Num. obs: 5918 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H0S Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.495 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.251 / 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: 12.344 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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