[English] 日本語
Yorodumi- PDB-6bu1: Crystal structure of Mycobacterium tuberculosis malate synthase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bu1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-Br-3-OH-phenyldiketoacid | ||||||
Components | Malate synthase G | ||||||
Keywords | STRUCTURAL GENOMICS / Transferase / Acetyltransferase / TB Structural Genomics Consortium / TBSGC / 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: 1.584 Å | ||||||
Authors | Krieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6bu1.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6bu1.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 6bu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bu1_validation.pdf.gz | 814.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6bu1_full_validation.pdf.gz | 818.3 KB | Display | |
Data in XML | 6bu1_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 6bu1_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/6bu1 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/6bu1 | HTTPS FTP |
-Related structure data
Related structure data | 6apzC 6as6C 6asuC 6au9C 6axbC 6ba7C 6c2xC 6c6oC 6c7bC 6c8pC 6dkoC 6dl9C 6dljC 6dnpC 1n8iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Production host: Escherichia coli (E. coli) References: UniProt: A5U3K4, UniProt: P9WK17*PLUS, malate synthase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-E9S / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.72 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Tris-HCl, MgCl2 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.584→50 Å / Num. obs: 88699 / % possible obs: 91.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.584→1.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 3.011 / Num. unique obs: 2728 / % possible all: 55.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N8I Resolution: 1.584→45.079 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.22
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.584→45.079 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|