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- PDB-4qe3: Crystal structure of Antigen 85C-H260Q mutant -

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Basic information

Entry
Database: PDB / ID: 4qe3
TitleCrystal structure of Antigen 85C-H260Q mutant
ComponentsDiacylglycerol acyltransferase/mycolyltransferase Ag85C
KeywordsTRANSFERASE / 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
ACETIC ACID / Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.351 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 15, 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7543
Polymers33,0621
Non-polymers6922
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.725, 68.128, 76.307
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: 33061.574 Da / Num. of mol.: 1 / Mutation: H260Q
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: Chemical ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3350, 0.1M sodium acetate trihydrate, 6mM CHAPSO, 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: 23-ID-D / Wavelength: 0.97936 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 379104 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 16.037
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.814 / Num. unique all: 379104 / Rsym value: 0.513 / % possible all: 85.5

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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: 1.351→38.153 Å / SU ML: 0.12 / σ(F): 1.33 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 3413 4.99 %RANDOM
Rwork0.1713 ---
obs0.1727 68398 97.68 %-
all-68398 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.351→38.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 30 234 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062199
X-RAY DIFFRACTIONf_angle_d1.1153014
X-RAY DIFFRACTIONf_dihedral_angle_d13.466767
X-RAY DIFFRACTIONf_chiral_restr0.048308
X-RAY DIFFRACTIONf_plane_restr0.007394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3508-1.37010.22281080.25122118X-RAY DIFFRACTION78
1.3701-1.39060.27321160.23272396X-RAY DIFFRACTION87
1.3906-1.41230.24351370.21832546X-RAY DIFFRACTION93
1.4123-1.43540.22951420.20872670X-RAY DIFFRACTION98
1.4354-1.46020.18991430.18952723X-RAY DIFFRACTION99
1.4602-1.48670.2021450.18032737X-RAY DIFFRACTION100
1.4867-1.51530.18181440.1792726X-RAY DIFFRACTION100
1.5153-1.54630.22441450.17032784X-RAY DIFFRACTION100
1.5463-1.57990.20131430.16222715X-RAY DIFFRACTION100
1.5799-1.61670.17221440.16122728X-RAY DIFFRACTION100
1.6167-1.65710.18491450.16062762X-RAY DIFFRACTION100
1.6571-1.70190.17691450.15962752X-RAY DIFFRACTION100
1.7019-1.7520.19491450.1722753X-RAY DIFFRACTION100
1.752-1.80850.21951440.16842749X-RAY DIFFRACTION100
1.8085-1.87310.18661460.16692755X-RAY DIFFRACTION100
1.8731-1.94810.17911450.16892762X-RAY DIFFRACTION99
1.9481-2.03680.18841450.16862759X-RAY DIFFRACTION100
2.0368-2.14420.17261460.16562781X-RAY DIFFRACTION100
2.1442-2.27850.20091400.16792687X-RAY DIFFRACTION96
2.2785-2.45440.20581460.16952779X-RAY DIFFRACTION100
2.4544-2.70130.22131490.17942819X-RAY DIFFRACTION100
2.7013-3.09210.19431470.17632807X-RAY DIFFRACTION100
3.0921-3.89510.20591470.16792757X-RAY DIFFRACTION97
3.8951-38.16870.18941560.1582920X-RAY DIFFRACTION98

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