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- PDB-4mql: Crystal structure of Antigen 85C-C209S mutant -

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Basic information

Entry
Database: PDB / ID: 4mql
TitleCrystal structure of Antigen 85C-C209S mutant
ComponentsDiacylglycerol acyltransferase/mycolyltransferase Ag85C
KeywordsTRANSFERASE / 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 / Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFavrot, L. / Grzegorzewicz, A.E. / Lajiness, D.H. / Marvin, R.K. / Boucau, J. / Isailovic, D. / Jackson, M. / Ronning, D.R.
CitationJournal: 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
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Feb 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

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Assembly

Deposited unit
A: Diacylglycerol acyltransferase/mycolyltransferase Ag85C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7163
Polymers33,2981
Non-polymers4182
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.764, 68.171, 35.908
Angle α, β, γ (deg.)90.00, 94.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

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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: 33297.797 Da / Num. of mol.: 1 / Mutation: C255S
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
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M bis-tris 6.5, 25% PEG 3350, 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 29, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 79869 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 51.408

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.086 Å / SU ML: 0.08 / σ(F): 1.37 / Phase error: 14.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1646 3979 4.98 %
Rwork0.1534 --
obs0.154 79862 99.6 %
all-103943 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→34.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 28 278 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062311
X-RAY DIFFRACTIONf_angle_d1.143160
X-RAY DIFFRACTIONf_dihedral_angle_d19.019850
X-RAY DIFFRACTIONf_chiral_restr0.048311
X-RAY DIFFRACTIONf_plane_restr0.007419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31580.18641270.17942645X-RAY DIFFRACTION96
1.3158-1.33250.16731430.17022691X-RAY DIFFRACTION99
1.3325-1.350.1871430.16572661X-RAY DIFFRACTION100
1.35-1.36850.16961380.16772726X-RAY DIFFRACTION100
1.3685-1.38810.18241360.17092730X-RAY DIFFRACTION100
1.3881-1.40880.20441510.16762659X-RAY DIFFRACTION100
1.4088-1.43080.15921470.15992724X-RAY DIFFRACTION100
1.4308-1.45430.17421370.16012730X-RAY DIFFRACTION100
1.4543-1.47940.16591420.15662688X-RAY DIFFRACTION100
1.4794-1.50630.18371410.14852720X-RAY DIFFRACTION100
1.5063-1.53520.18721460.14462693X-RAY DIFFRACTION100
1.5352-1.56660.1551350.1462726X-RAY DIFFRACTION100
1.5666-1.60060.15671420.1432707X-RAY DIFFRACTION100
1.6006-1.63790.16071520.14622723X-RAY DIFFRACTION100
1.6379-1.67880.15561310.14682723X-RAY DIFFRACTION100
1.6788-1.72420.17471470.15372713X-RAY DIFFRACTION100
1.7242-1.77490.16691480.15352691X-RAY DIFFRACTION100
1.7749-1.83220.16131410.15442734X-RAY DIFFRACTION100
1.8322-1.89770.16631390.15822731X-RAY DIFFRACTION100
1.8977-1.97370.16121460.15522688X-RAY DIFFRACTION100
1.9737-2.06350.14451410.14942738X-RAY DIFFRACTION100
2.0635-2.17230.15921550.15392693X-RAY DIFFRACTION100
2.1723-2.30830.18811400.15472729X-RAY DIFFRACTION100
2.3083-2.48650.15751370.15882744X-RAY DIFFRACTION100
2.4865-2.73670.16251480.16532740X-RAY DIFFRACTION100
2.7367-3.13240.16881470.16072712X-RAY DIFFRACTION100
3.1324-3.94560.16511390.14482690X-RAY DIFFRACTION97
3.9456-34.09720.14751400.13932734X-RAY DIFFRACTION97

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