+Open data
-Basic information
Entry | Database: PDB / ID: 4mqm | ||||||
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Title | Crystal structure of Antigen 85C in presence of Ebselen | ||||||
Components | Diacylglycerol acyltransferase/mycolyltransferase Ag85C | ||||||
Keywords | TRANSFERASE / 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: 1.346 Å | ||||||
Authors | Favrot, L. / Grzegorzewicz, A.E. / Lajiness, D.H. / Marvin, R.K. / Boucau, J. / Isailovic, D. / Jackson, M. / Ronning, D.R. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Mechanism of inhibition of Mycobacterium tuberculosis antigen 85 by ebselen. Authors: Favrot, L. / Grzegorzewicz, A.E. / Lajiness, D.H. / Marvin, R.K. / Boucau, J. / Isailovic, D. / Jackson, M. / 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 | 4mqm.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mqm.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/4mqm ftp://data.pdbj.org/pub/pdb/validation_reports/mq/4mqm | HTTPS FTP |
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-Related 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: 33313.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fbpC, mpt45, Rv0129c, MT0137, MTCI5.03c / Production host: Escherichia coli (E. coli) References: UniProt: P0A4V4, UniProt: P9WQN9*PLUS, 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: 2.33 Å3/Da / Density % sol: 47.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 1500, pH 7.5, 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: 0.97922 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.346→50 Å / Num. obs: 68823 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.35→50 Å / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.346→29.696 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 19.07 / 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: 1.346→29.696 Å
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Refine LS restraints |
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LS refinement shell |
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