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Yorodumi- PDB-4qdt: Crystal structure of Antigen 85C co-crystallized with iodoacetamide -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qdt | ||||||
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Title | Crystal structure of Antigen 85C co-crystallized with iodoacetamide | ||||||
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 / mycolate cell wall layer assembly / glycolipid biosynthetic process / 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 / mycolate cell wall layer assembly / glycolipid biosynthetic process / 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: 1.498 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 | 4qdt.cif.gz | 117.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qdt.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qdt_validation.pdf.gz | 425.1 KB | Display | wwPDB validaton report |
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Full document | 4qdt_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 4qdt_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4qdt_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/4qdt ftp://data.pdbj.org/pub/pdb/validation_reports/qd/4qdt | HTTPS FTP |
-Related structure data
Related structure data | 4qdoC 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: 32997.449 Da / Num. of mol.: 1 / Fragment: UNP residues 46-340 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: 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: 2.39 Å3/Da / Density % sol: 48.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.1M bis-tris, 0.2M lithium sulfate monohydrate, pH 5.5, 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-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2013 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 375222 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.667 / Num. unique all: 375222 / Rsym value: 0.37 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.498→31.07 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 14.89 / 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: 1.498→31.07 Å
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Refine LS restraints |
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LS refinement shell |
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