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- PDB-3saz: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3saz | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(3-bromophenyl)-2,4-dioxobutanoic acid inhibitor | ||||||
![]() | Malate synthase G | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / malate synthase / TRANSFERASE-TRANSFERASE 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 / manganese ion binding / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krieger, I.V. / Sun, Q. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) | ||||||
![]() | ![]() 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 | ![]() | 126.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 708.2 KB | Display | ![]() |
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Full document | ![]() | 714.2 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s9iC ![]() 3s9zC ![]() 3sadC ![]() 3sb0C ![]() 1n8iS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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: P0A5J4, UniProt: P9WK17*PLUS, malate synthase | ||||
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#2: Chemical | ChemComp-043 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | DEVIATIONS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.12 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 3350, 0.1 M magnesium chloride, 0.1 M TRIS-HCl , VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: 2 x 2 mosaic CCD detector / Detector: CCD / Date: Feb 9, 2008 |
Radiation | Monochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→49.57 Å / Num. all: 56204 / Num. obs: 56104 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Rmerge(I) obs: 0.099 / Rsym value: 0.066 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.785 / % possible all: 40.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1N8I Resolution: 2.04→49.57 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.9497 / SU ML: 0.22 / σ(F): 1.89 / Phase error: 19.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.899 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.192 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→49.57 Å
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Refine LS restraints |
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LS refinement shell |
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