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Yorodumi- PDB-4qdo: Crystal structure of Ag85C co-crystallized with p-chloromercuribe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qdo | ||||||
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Title | Crystal structure of Ag85C co-crystallized with p-chloromercuribenzoic acid | ||||||
Components | Diacylglycerol acyltransferase/mycolyltransferase Ag85C | ||||||
Keywords | TRANSFERASE / mycolyltransferase / Diacylglycerol acyltransferase | ||||||
Function / homology | Function and homology information trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / glycolipid biosynthetic process / mycolate cell wall layer assembly / zymogen binding / lipid transport / acyltransferase activity, transferring groups other than amino-acyl groups / peptidoglycan-based cell wall ...trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / glycolipid biosynthetic process / mycolate cell wall layer assembly / zymogen binding / lipid transport / acyltransferase activity, transferring groups other than amino-acyl groups / peptidoglycan-based cell wall / response to antibiotic / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å | ||||||
Authors | Favrot, L. / Lajiness, D.H. / Ronning, D.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Inactivation of the Mycobacterium tuberculosis Antigen 85 Complex by Covalent, Allosteric Inhibitors. Authors: Favrot, L. / Lajiness, D.H. / Ronning, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qdo.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qdo.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/4qdo ftp://data.pdbj.org/pub/pdb/validation_reports/qd/4qdo | HTTPS FTP |
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-Related structure data
Related structure data | 4qdtC 4qduC 4qdxC 4qdzC 4qe3C 4qekC 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
#1: Protein | Mass: 33392.285 Da / Num. of mol.: 1 Fragment: Diacylglycerol acyltransferase/mycolyltransferase Ag85C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fbpC, mpt45, MTCI5.03c, Rv0129c / Production host: Escherichia coli (E. coli) References: UniProt: P9WQN9, trehalose O-mycolyltransferase, diacylglycerol O-acyltransferase |
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#2: Chemical | ChemComp-ACT / |
#3: 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: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 3350, 0.1M sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2013 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 5.84 / Num. unique all: 320135 / Rsym value: 0.458 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.899→47.024 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 27.31 / 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: 1.899→47.024 Å
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Refine LS restraints |
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LS refinement shell |
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