[English] 日本語
Yorodumi- PDB-5t8g: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t8g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-oxo-4-((thiophene-2-carbonyl)oxy)butanoic acid | |||||||||
Components | Malate synthase G | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / transferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR 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 / 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: 2.04 Å | |||||||||
Authors | Huang, H.-L. / Sacchetiini, J.C. | |||||||||
Funding support | United States, 1items
| |||||||||
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: 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. #2: 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. / Ioerger, T.R. / Sacchettini, J.C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5t8g.cif.gz | 165.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5t8g.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t8g_validation.pdf.gz | 442.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5t8g_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 5t8g_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 5t8g_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8g ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8g | 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 5ecvC 5h8mC 5h8pC 5h8uC 1n8iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-4Z0 / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG3350, MgCl2, tris buffer / PH range: 7.0-8.5 / Temp details: Varies between 289-290 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Varies between 100-120 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→45.78 Å / Num. obs: 46135 / % possible obs: 99.36 % / Redundancy: 13.5 % / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.04→2.08 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 4.07 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 2.04→35.011 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.52
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→35.011 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|