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- PDB-7myg: M. tb Ag85C modified by THL-10d -

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Basic information

Entry
Database: PDB / ID: 7myg
TitleM. tb Ag85C modified by THL-10d
ComponentsDiacylglycerol acyltransferase
KeywordsTRANSFERASE / Mycolyltransferase / Alpha/Beta-hydrolase fold
Function / homology
Function and homology information


trehalose O-mycolyltransferase / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / extracellular region / membrane
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Diacylglycerol acyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSudasinghe, T.D. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI105084 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Total Synthesis of Tetrahydrolipstatin, Its Derivatives, and Evaluation of Their Ability to Potentiate Multiple Antibiotic Classes against Mycobacterium Species.
Authors: Khan, S.S. / Sudasinghe, T.D. / Landgraf, A.D. / Ronning, D.R. / Sucheck, S.J.
History
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diacylglycerol acyltransferase
B: Diacylglycerol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,47916
Polymers61,1902
Non-polymers1,28914
Water2,198122
1
A: Diacylglycerol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2398
Polymers30,5951
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diacylglycerol acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2398
Polymers30,5951
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.458, 70.606, 68.590
Angle α, β, γ (deg.)90.000, 89.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 259 or resid 261 through 282))
21(chain B and (resid 7 through 259 or resid 261 through 282))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR(chain A and (resid 7 through 259 or resid 261 through 282))AA7 - 2593 - 255
12SERSERGLYGLY(chain A and (resid 7 through 259 or resid 261 through 282))AA261 - 282257 - 278
21PROPROTHRTHR(chain B and (resid 7 through 259 or resid 261 through 282))BB7 - 2593 - 255
22SERSERGLYGLY(chain B and (resid 7 through 259 or resid 261 through 282))BB261 - 282257 - 278

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Components

#1: Protein Diacylglycerol acyltransferase / Diacylglycerol acyltransferase/mycolyltransferase Ag85A / Diacylglycerol ...Diacylglycerol acyltransferase/mycolyltransferase Ag85A / Diacylglycerol acyltransferase/mycolyltransferase Ag85C / Esterase family protein / Secreted antigen 85-C FbpC (85C) (Antigen 85 complex C) (Ag58C) (Mycolyl transferase 85C) (Fibronectin-binding protein C)


Mass: 30594.809 Da / Num. of mol.: 2 / Mutation: S152G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: fbpC, fbpC_1, DSI38_14625, E5M05_00190, E5M52_01085, E5M78_01085, ERS007657_00618, ERS007663_00913, ERS007665_00182, ERS007703_02124, ERS007722_01715, ERS007741_01210, ERS013471_00870, ...Gene: fbpC, fbpC_1, DSI38_14625, E5M05_00190, E5M52_01085, E5M78_01085, ERS007657_00618, ERS007663_00913, ERS007665_00182, ERS007703_02124, ERS007722_01715, ERS007741_01210, ERS013471_00870, ERS024276_00850, ERS027659_01767, ERS094182_00158, F6W99_02771, FRD82_05760, GCL30_02455, SAMEA2683035_00278
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045JX50, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% v/v Tacsimate (pH 7.0) and 20 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.51→59.46 Å / Num. obs: 19458 / % possible obs: 97.98 % / Redundancy: 5.5 % / CC1/2: 0.822 / Net I/σ(I): 15.35
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 5.2 % / Num. unique obs: 1920 / CC1/2: 0.222 / % possible all: 94.32

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQZ

1dqz


Resolution: 2.51→59.46 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1947 10.13 %
Rwork0.1555 17279 -
obs0.1623 19226 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.39 Å2 / Biso mean: 28.7354 Å2 / Biso min: 13.71 Å2
Refinement stepCycle: final / Resolution: 2.51→59.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 84 122 4351
Biso mean--42.76 34.16 -
Num. residues----530
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2430X-RAY DIFFRACTION4.966TORSIONAL
12B2430X-RAY DIFFRACTION4.966TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.570.28581310.13991159129093
2.57-2.640.28931310.14191191132295
2.64-2.720.24421270.15081210133795
2.72-2.810.23981350.15081220135597
2.81-2.910.22571440.15451190133497
2.91-3.020.24321390.14941221136097
3.02-3.160.231300.15281236136698
3.16-3.330.18811400.14161245138599
3.33-3.530.22351410.135712591400100
3.53-3.810.19181370.144912661403100
3.81-4.190.22561470.157912651412100
4.19-4.80.21191460.16112561402100
4.8-6.040.19641380.181412831421100
6.04-59.460.2311610.17371278143999

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