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Yorodumi- PDB-5e9x: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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-Basic information
Entry | Database: PDB / ID: 5e9x | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-chloro-6H-thieno[2,3-b]pyrrole-5-carboxylic acid | ||||||
Components | Malate synthase G | ||||||
Keywords | TRANSFERASE / Complex | ||||||
Function / homology | Function and homology information host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / glyoxylate catabolic process / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / glyoxylate catabolic process / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.943 Å | ||||||
Authors | Huang, H.-L. / Sacchettini, J.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2016 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: Journal: Chem. Biol. / Year: 2012 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. / Loerger, T.R. / Sacchettini, J.C. #2: Journal: J. Biol. Chem. / Year: 2003 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e9x.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e9x.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e9x_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
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Full document | 5e9x_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 5e9x_validation.xml.gz | 31 KB | Display | |
Data in CIF | 5e9x_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/5e9x ftp://data.pdbj.org/pub/pdb/validation_reports/e9/5e9x | 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 5ecvC 5h8mC 5h8pC 5h8uC 5t8gC 1n8iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: glcB, Rv1837c, MTCY1A11.06 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P9WK17, malate synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-5LA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.58 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, magnesium chloride, tris / 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2013 |
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: 1.94→45.87 Å / Num. all: 56811 / Num. obs: 56204 / % possible obs: 98.63 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.344 / Rsym value: 0.0354 / Net I/av σ(I): 77.7 / Net I/σ(I): 14.61 |
Reflection shell | Resolution: 1.94→2.05 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.27 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 1.943→35.917 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.92 / 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: 1.943→35.917 Å
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Refine LS restraints |
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LS refinement shell |
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