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- PDB-5cc3: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cc3 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 6-bromo-1H-indole-2-carboxylic acid | ||||||
![]() | Malate synthase G | ||||||
![]() | TRANSFERASE / Complex / Fragment | ||||||
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 catabolic process / glyoxylate cycle / 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 catabolic 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, H.-L. / Sacchettini, J.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of fragment-bound malate synthase from Mycobacterium tuberculosis provide insights into mechanism and potential inhibitor designs Authors: Huang, H.-L. / Krieger, I.V. / Gawandi, V.B. / Parai, M. / 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 | ![]() | 165.1 KB | Display | ![]() |
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PDB format | ![]() | 126.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5cc5C ![]() 5cc6C ![]() 5cc7C ![]() 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.) ![]() Strain: ATCC 25618 / H37Rv / Gene: glcB, Rv1837c, MTCY1A11.06 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-4ZU / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.29 % |
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Crystal grow | Temperature: 300 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: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 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: 2.2→44.46 Å / Num. all: 36302 / Num. obs: 31603 / % possible obs: 87.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.776 Å2 / Rsym value: 0.0395 / Net I/σ(I): 20.28 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.7 % / % possible all: 72.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N8I Resolution: 2.204→44.46 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.26 / 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: 2.204→44.46 Å
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Refine LS restraints |
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LS refinement shell |
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