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Yorodumi- PDB-3s9z: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
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-Basic information
Entry | Database: PDB / ID: 3s9z | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-bromophenyl)-2,4-dioxobutanoic acid inhibitor | ||||||
Components | Malate synthase G | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitor complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / malate synthase / 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 catabolic process / glyoxylate cycle / 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 catabolic process / glyoxylate cycle / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / manganese ion binding / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.793 Å | ||||||
Authors | Krieger, I.V. / Sun, Q. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) | ||||||
Citation | 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s9z.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s9z.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/3s9z ftp://data.pdbj.org/pub/pdb/validation_reports/s9/3s9z | HTTPS FTP |
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-Related structure data
Related structure data | 3s9iC 3sadC 3sazC 3sb0C 1n8iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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 / Mutation: c619A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glcB, GlcB (Rv1837c), MT1885, MTCY1A11.06, Rv1837c / Production host: Escherichia coli (E. coli) References: UniProt: P0A5J4, UniProt: P9WK17*PLUS, malate synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-I92 / | #4: Water | ChemComp-HOH / | Compound details | LIGAND I92 WAS BUILD TO MAXIMIZE AGREEMENT WITH THE DENSITY. DEVIATIONS FROM SP2 GEOMETRY ...LIGAND I92 WAS BUILD TO MAXIMIZE AGREEMENT WITH THE DENSITY. DEVIATIONS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.57 % |
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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 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97933 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2009 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→45.05 Å / Num. all: 73112 / Num. obs: 72929 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.192 / Rsym value: 0.196 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 1 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.728 / % possible all: 79 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1N8I Resolution: 1.793→45.05 Å / Cor.coef. Fo:Fc: 0.9613 / Cor.coef. Fo:Fc free: 0.9474 / SU ML: 0.18 / σ(F): 1.33 / Phase error: 23.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.231 Å2 / ksol: 0.293 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.203 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.793→45.05 Å
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Refine LS restraints |
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LS refinement shell |
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