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- PDB-5ecv: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ecv | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-hydroxy-4-(4-methyl-1H-indol-5-yl)-4-oxobut-2-enoic acid | ||||||
![]() | Malate synthase G | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / glyoxylate catabolic process / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / glyoxylate catabolic process / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krieger, I.V. / Huang, H.-L. / Sacchettini, J.C. | ||||||
![]() | ![]() Title: Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange. Authors: Huang, H.L. / Krieger, I.V. / Parai, M.K. / Gawandi, V.B. / Sacchettini, J.C. #1: ![]() Title: Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis. Authors: Smith, C.V. / Huang, C.C. / Miczak, A. / Russell, D.G. / Sacchettini, J.C. / Honer zu Bentrup, K. #2: ![]() Title: Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase. Authors: Krieger, I.V. / Freundlich, J.S. / Gawandi, V.B. / Roberts, J.P. / Gawandi, V.B. / Sun, Q. / Owen, J.L. / Fraile, M.T. / Huss, S.I. / Lavandera, J.L. / Ioerger, T.R. / Sacchettini, J.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 | ![]() | 163.2 KB | Display | ![]() |
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PDB format | ![]() | 125.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c7vC ![]() 5c9rC ![]() 5c9uC ![]() 5c9wC ![]() 5c9xC ![]() 5cahC ![]() 5cakC ![]() 5cbbC ![]() 5cbiC ![]() 5cbjC ![]() 5cczC ![]() 5cewC ![]() 5cjmC ![]() 5cjnC ![]() 5drcC ![]() 5driC ![]() 5dx7C ![]() 5e9xC ![]() 5h8mC ![]() 5h8pC ![]() 5h8uC ![]() 5t8gC ![]() 1n8iS 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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Unit cell |
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Components
#1: Protein | Mass: 80456.734 Da / Num. of mol.: 1 / Mutation: C619A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-5M2 / (~{ |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, magnesium chloride, tris-HCl / PH range: 7.0-8.5 / Temp details: Varies between 289-291 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→44.213 Å / Num. all: 42010 / Num. obs: 41059 / % possible obs: 97.7 % / Redundancy: 6.5 % / Rsym value: 0.064 / Net I/av σ(I): 26.1 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.08→2.12 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.17 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N8I Resolution: 2.085→44.213 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.085→44.213 Å
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Refine LS restraints |
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LS refinement shell |
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