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- PDB-4qdt: Crystal structure of Antigen 85C co-crystallized with iodoacetamide -

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Basic information

Entry
Database: PDB / ID: 4qdt
TitleCrystal structure of Antigen 85C co-crystallized with iodoacetamide
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
Diacylglycerol acyltransferase/mycolyltransferase Ag85C
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 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
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

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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)32,9971
Polymers32,9971
Non-polymers00
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)60.777, 68.039, 76.279
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: 32997.449 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.: 234 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.1M bis-tris, 0.2M lithium sulfate monohydrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 375222 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.667 / Num. unique all: 375222 / Rsym value: 0.37 / % possible all: 100

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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: 1.498→31.07 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 14.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1752 1999 3.89 %RANDOM
Rwork0.1465 ---
obs0.1476 51343 99.58 %-
all-51343 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.498→31.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 0 234 2370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062231
X-RAY DIFFRACTIONf_angle_d1.0753055
X-RAY DIFFRACTIONf_dihedral_angle_d12.876787
X-RAY DIFFRACTIONf_chiral_restr0.048305
X-RAY DIFFRACTIONf_plane_restr0.007407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4976-1.53510.19431330.14223301X-RAY DIFFRACTION95
1.5351-1.57660.15531420.11613490X-RAY DIFFRACTION100
1.5766-1.6230.13711430.10513525X-RAY DIFFRACTION100
1.623-1.67540.16191420.10533497X-RAY DIFFRACTION100
1.6754-1.73520.16181410.11253489X-RAY DIFFRACTION100
1.7352-1.80470.14411420.1263492X-RAY DIFFRACTION100
1.8047-1.88680.1511430.1323534X-RAY DIFFRACTION100
1.8868-1.98630.19831420.13753501X-RAY DIFFRACTION100
1.9863-2.11070.1741430.14343527X-RAY DIFFRACTION100
2.1107-2.27360.17981440.14473544X-RAY DIFFRACTION100
2.2736-2.50230.17781430.15313540X-RAY DIFFRACTION100
2.5023-2.86420.18991440.16313581X-RAY DIFFRACTION100
2.8642-3.60780.18771470.16813608X-RAY DIFFRACTION100
3.6078-31.07630.17061500.14793715X-RAY DIFFRACTION99

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