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- PDB-6dl9: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dl9 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2,6-Cl-phenyldiketoacid | ||||||
![]() | Malate synthase G | ||||||
![]() | LYASE/LYASE inhibitor / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex / LYASE / PSI-2 / Protein Structure Initiative / LYASE-LYASE inhibitor complex | ||||||
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 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163 KB | Display | ![]() |
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PDB format | ![]() | 124.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.7 KB | Display | ![]() |
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Full document | ![]() | 795.1 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6apzC ![]() 6as6C ![]() 6asuC ![]() 6au9C ![]() 6axbC ![]() 6ba7C ![]() 6bu1C ![]() 6c2xC ![]() 6c6oC ![]() 6c7bC ![]() 6c8pC ![]() 6dkoC ![]() 6dljC ![]() 6dnpC ![]() 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.) ![]() ![]() ![]() ![]() References: UniProt: A0A045ITM4, UniProt: P9WK17*PLUS, malate synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GXD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, TRIS-HCl, MgCl2 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 56595 / % possible obs: 86.9 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 995 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N8I Resolution: 1.8→49.472 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→49.472 Å
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Refine LS restraints |
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LS refinement shell |
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