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- PDB-4qdo: Crystal structure of Ag85C co-crystallized with p-chloromercuribe... -

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Basic information

Entry
Database: PDB / ID: 4qdo
TitleCrystal structure of Ag85C co-crystallized with p-chloromercuribenzoic acid
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 / acyltransferase activity, transferring groups other than amino-acyl groups / lipid transport / 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 / acyltransferase activity, transferring groups other than amino-acyl groups / lipid transport / peptidoglycan-based cell wall / response to antibiotic / extracellular region / membrane
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
ACETATE ION / Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 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
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4512
Polymers33,3921
Non-polymers591
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.701, 67.988, 74.365
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: 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.92 %
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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 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

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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: 1.899→47.024 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1978 8.19 %RANDOM
Rwork0.1929 ---
obs0.1967 24160 96.97 %-
all-24160 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→47.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 4 108 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092194
X-RAY DIFFRACTIONf_angle_d1.4052998
X-RAY DIFFRACTIONf_dihedral_angle_d16.386775
X-RAY DIFFRACTIONf_chiral_restr0.053299
X-RAY DIFFRACTIONf_plane_restr0.007396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8988-1.94630.55771200.46181314X-RAY DIFFRACTION83
1.9463-1.99890.29031420.24941575X-RAY DIFFRACTION98
1.9989-2.05770.25531430.18721618X-RAY DIFFRACTION100
2.0577-2.12410.2241430.19471613X-RAY DIFFRACTION100
2.1241-2.20.22091430.18411594X-RAY DIFFRACTION100
2.2-2.28810.32461290.23021473X-RAY DIFFRACTION90
2.2881-2.39230.27031430.18191604X-RAY DIFFRACTION100
2.3923-2.51840.25881450.19651619X-RAY DIFFRACTION100
2.5184-2.67610.25451450.18821630X-RAY DIFFRACTION100
2.6761-2.88270.22191450.20021630X-RAY DIFFRACTION100
2.8827-3.17280.25651470.20121637X-RAY DIFFRACTION100
3.1728-3.63180.23481450.19591643X-RAY DIFFRACTION99
3.6318-4.5750.21041430.16271586X-RAY DIFFRACTION94
4.575-47.03870.18341450.16141646X-RAY DIFFRACTION93

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