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- PDB-4qdu: Crystal structure of Antigen 85C co-crystallized with ebselen -

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Basic information

Entry
Database: PDB / ID: 4qdu
TitleCrystal structure of Antigen 85C co-crystallized with ebselen
ComponentsDiacylglycerol acyltransferase/mycolyltransferase Ag85C
KeywordsTRANSFERASE / alpha/beta-hydrolase fold / mycolyltransferase / Diacylglycerol acyltransferase
Function / homology
Function and homology information


trehalose O-mycolyltransferase activity / trehalose O-mycolyltransferase / 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 activity / trehalose O-mycolyltransferase / 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
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFavrot, L. / Lajiness, D.H. / Ronning, D.R.
CitationJournal: 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
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diacylglycerol acyltransferase/mycolyltransferase Ag85C


Theoretical massNumber of molelcules
Total (without water)33,2701
Polymers33,2701
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.471, 67.786, 75.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diacylglycerol acyltransferase/mycolyltransferase Ag85C / DGAT / Acyl-CoA:diacylglycerol acyltransferase / Antigen 85 complex C / 85C / Ag85C / Fibronectin- ...DGAT / Acyl-CoA:diacylglycerol acyltransferase / Antigen 85 complex C / 85C / Ag85C / Fibronectin-binding protein C / Fbps C


Mass: 33269.668 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07818 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07818 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 384079 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 5.414 / Rsym value: 0.304 / % possible all: 90.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→37.604 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 16.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 2000 3.35 %RANDOM
Rwork0.1458 ---
obs0.147 59653 98.48 %-
all-59653 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→37.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 0 279 2489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062315
X-RAY DIFFRACTIONf_angle_d1.0953172
X-RAY DIFFRACTIONf_dihedral_angle_d13.758825
X-RAY DIFFRACTIONf_chiral_restr0.047314
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3999-1.43490.20811270.15983646X-RAY DIFFRACTION88
1.4349-1.47370.17561380.15034006X-RAY DIFFRACTION97
1.4737-1.51710.20451430.13694102X-RAY DIFFRACTION100
1.5171-1.5660.19211450.12474157X-RAY DIFFRACTION100
1.566-1.6220.16251410.1194086X-RAY DIFFRACTION100
1.622-1.68690.16781450.12124160X-RAY DIFFRACTION100
1.6869-1.76370.14771420.12854139X-RAY DIFFRACTION100
1.7637-1.85670.19831440.13544142X-RAY DIFFRACTION100
1.8567-1.9730.18031460.14264183X-RAY DIFFRACTION100
1.973-2.12540.16641440.14364167X-RAY DIFFRACTION100
2.1254-2.33920.1691450.1424190X-RAY DIFFRACTION100
2.3392-2.67760.19491470.15824207X-RAY DIFFRACTION100
2.6776-3.37320.18491470.16164253X-RAY DIFFRACTION100
3.3732-37.61760.18841460.14674215X-RAY DIFFRACTION95

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