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Yorodumi- PDB-6axb: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6axb | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-naphthyldiketoacid | ||||||
Components | Malate synthase G | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / 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 / 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 / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 6axb.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6axb.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 6axb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6axb_validation.pdf.gz | 725.3 KB | Display | wwPDB validaton report |
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Full document | 6axb_full_validation.pdf.gz | 731.1 KB | Display | |
Data in XML | 6axb_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 6axb_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/6axb ftp://data.pdbj.org/pub/pdb/validation_reports/ax/6axb | HTTPS FTP |
-Related structure data
Related structure data | 6apzC 6as6C 6asuC 6au9C 6ba7C 6bu1C 6c2xC 6c6oC 6c7bC 6c8pC 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) / Production host: Escherichia coli (E. coli) References: UniProt: A5U3K4, UniProt: P9WK17*PLUS, malate synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-C0V / ( | #4: Chemical | #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: 2.23 Å3/Da / Density % sol: 44.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MgCl2, TRIS-HCl / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 66439 / % possible obs: 92.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.78→1.81 Å / Rmerge(I) obs: 2.858 / Num. unique obs: 1669 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 1.8→45.152 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.152 Å
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Refine LS restraints |
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LS refinement shell |
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