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Yorodumi- PDB-6apz: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6apz | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 3-hydroxy-phenyldiketoacid | ||||||
Components | Malate synthase G | ||||||
Keywords | TRANSFERASE / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information malate synthase / malate synthase activity / glyoxylate cycle / tricarboxylic acid cycle / cell surface / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.254 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 | 6apz.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6apz.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 6apz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6apz_validation.pdf.gz | 937.1 KB | Display | wwPDB validaton report |
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Full document | 6apz_full_validation.pdf.gz | 942.5 KB | Display | |
Data in XML | 6apz_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 6apz_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6apz ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apz | HTTPS FTP |
-Related structure data
Related structure data | 6as6C 6asuC 6au9C 6axbC 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
-Protein , 1 types, 1 molecules A
#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 (strain ATCC 25177 / H37Ra) (bacteria) Strain: ATCC 25177 / H37Ra / Gene: glcB, MRA_1848 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U3K4, malate synthase |
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-Non-polymers , 5 types, 300 molecules
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-BQ4 / ( | ||
#4: Chemical | ChemComp-NI / | ||
#5: Chemical | ChemComp-PEG / #6: 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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: MgCl2, TRIS-HCl, PEG3350 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Nov 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→50 Å / Num. obs: 26910 / % possible obs: 72.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.22→2.26 Å / Rmerge(I) obs: 0.823 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 2.254→45.022 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.254→45.022 Å
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Refine LS restraints |
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LS refinement shell |
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