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- PDB-5kwi: M.tb Ag85C modified at C209 by adamantyl-ebselen -

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Open data


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Basic information

Entry
Database: PDB / ID: 5kwi
TitleM.tb Ag85C modified at C209 by adamantyl-ebselen
ComponentsDiacylglycerol acyltransferase/mycolyltransferase Ag85C
KeywordsTRANSFERASE / covalent Inhibitor / Acyl-transferase
Function / homology
Function and homology information


trehalose O-mycolyltransferase / trehalose O-mycolyltransferase activity / 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 / trehalose O-mycolyltransferase activity / 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
~{N}-(1-adamantyl)-2-selanyl-benzamide / 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
AuthorsGoins, C.M. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 United States
CitationJournal: ACS Infect Dis / Year: 2017
Title: Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives.
Authors: Goins, C.M. / Dajnowicz, S. / Thanna, S. / Sucheck, S.J. / Parks, J.M. / Ronning, D.R.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,5772
Polymers33,2431
Non-polymers3341
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.405, 63.405, 160.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 33242.785 Da / Num. of mol.: 1 / Fragment: UNP residues 47-340
Source method: isolated from a genetically manipulated source
Details: Adamantyl Ebselen derivative / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fbpC, mpt45, MT0137 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WQN8, UniProt: P9WQN9*PLUS, trehalose O-mycolyltransferase, diacylglycerol O-acyltransferase
#2: Chemical ChemComp-6Y1 / ~{N}-(1-adamantyl)-2-selanyl-benzamide / Adamantyl Ebselen (open form)


Mass: 334.315 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C17H21NOSe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 25 % w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3→40.85 Å / Num. obs: 81206 / % possible obs: 99.9 % / Redundancy: 13 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIXDEV_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QDU

4qdu


Resolution: 1.3→40.85 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.176 1998 2.46 %
Rwork0.166 --
obs0.166 81192 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 20 286 2509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062317
X-RAY DIFFRACTIONf_angle_d1.1553174
X-RAY DIFFRACTIONf_dihedral_angle_d13.479812
X-RAY DIFFRACTIONf_chiral_restr0.08316
X-RAY DIFFRACTIONf_plane_restr0.007420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2997-1.33220.22721390.22265504X-RAY DIFFRACTION100
1.3322-1.36820.22521410.19265592X-RAY DIFFRACTION100
1.3682-1.40850.21361400.17835588X-RAY DIFFRACTION100
1.4085-1.4540.18041410.16495560X-RAY DIFFRACTION100
1.454-1.50590.18571400.15795581X-RAY DIFFRACTION100
1.5059-1.56620.17141410.15375597X-RAY DIFFRACTION100
1.5662-1.63750.16481410.155609X-RAY DIFFRACTION100
1.6375-1.72390.16721430.15555629X-RAY DIFFRACTION100
1.7239-1.83190.21531420.16025622X-RAY DIFFRACTION100
1.8319-1.97330.21021420.16535657X-RAY DIFFRACTION100
1.9733-2.17190.18071440.16865664X-RAY DIFFRACTION100
2.1719-2.48610.16931450.16685741X-RAY DIFFRACTION100
2.4861-3.13210.18681460.17945786X-RAY DIFFRACTION100
3.1321-40.86590.14961530.15836064X-RAY DIFFRACTION100

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