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Yorodumi- PDB-5c9u: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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-Basic information
Entry | Database: PDB / ID: 5c9u | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-(2-(2,4-dichlorophenyl)hydrazinyl)-2-oxoacetic acid | ||||||
Components | Malate synthase G | ||||||
Keywords | TRANSFERASE / Fragment / Complex / acetyl-transferase | ||||||
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 / 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Huang, H.-L. / Sacchettini, J.C. | ||||||
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. / Sun, Q. / Owen, J.L. / Fraile, M.T. / Huss, S.I. / Lavandera, J.L. / Ioerger, 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 | 5c9u.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c9u.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 5c9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c9u_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 5c9u_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 5c9u_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 5c9u_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c9u ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9u | HTTPS FTP |
-Related structure data
Related structure data | 5c7vC 5c9rC 5c9wC 5c9xC 5cahC 5cakC 5cbbC 5cbiC 5cbjC 5cczC 5cewC 5cjmC 5cjnC 5drcC 5driC 5dx7C 5e9xC 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 / Plasmid: p6HisF11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P9WK17, malate synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-4Z1 / [ | #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: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, magnesium chloride, tris / PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→44.681 Å / Num. obs: 49254 / % possible obs: 93.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 18.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 1.95→44.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.28 / 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: 1.95→44.68 Å
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Refine LS restraints |
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LS refinement shell |
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