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Yorodumi- PDB-6c8p: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c8p | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-F-phenyldiketoacid | ||||||
Components | Malate synthase G | ||||||
Keywords | TRANSFERASE / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / 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: 1.635 Å | ||||||
Authors | Krieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | United States, 1items
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Citation | Journal: J Chem Inf Model / Year: 2018 Title: Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids. Authors: Ellenbarger, J.F. / Krieger, I.V. / Huang, H.L. / Gomez-Coca, S. / Ioerger, T.R. / Sacchettini, J.C. / Wheeler, S.E. / Dunbar, K.R. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c8p.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c8p.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 6c8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c8p_validation.pdf.gz | 749.8 KB | Display | wwPDB validaton report |
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Full document | 6c8p_full_validation.pdf.gz | 754.2 KB | Display | |
Data in XML | 6c8p_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 6c8p_validation.cif.gz | 47.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/6c8p ftp://data.pdbj.org/pub/pdb/validation_reports/c8/6c8p | HTTPS FTP |
-Related structure data
Related structure data | 6apzC 6as6C 6asuC 6au9C 6axbC 6ba7C 6bu1C 6c2xC 6c6oC 6c7bC 6dkoC 6dl9C 6dljC 6dnpC 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glcB / Production host: Escherichia coli (E. coli) References: UniProt: A5U3K4, UniProt: P9WK17*PLUS, malate synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EQA / ( | #4: Chemical | ChemComp-PEG / | #5: 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: 2.17 Å3/Da / Density % sol: 43.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: TRIS-HCl, MgCl2, PEG3350 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.635→74.34 Å / Num. obs: 88365 / % possible obs: 84.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.62→1.635 Å / Rmerge(I) obs: 1.236 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 1.635→44.696 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.635→44.696 Å
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Refine LS restraints |
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LS refinement shell |
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