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- PDB-7ryt: Crystal structure of Mycobacterium tuberculosis acetylated Homose... -

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Basic information

Entry
Database: PDB / ID: 7ryt
TitleCrystal structure of Mycobacterium tuberculosis acetylated Homoserine transacetylase with Coenzyme A
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / Alpha beta hydrolase / acetylated / acetyl tansferase / PROTEIN BINDING
Function / homology
Function and homology information


homoserine metabolic process / homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / methionine biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
COENZYME A / DI(HYDROXYETHYL)ETHER / Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsJayasinghe, Y.P. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI151924 United States
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Structural and Functional Characterization of Mycobacterium tuberculosis Homoserine Transacetylase.
Authors: Sharma, S. / Jayasinghe, Y.P. / Mishra, N.K. / Orimoloye, M.O. / Wong, T.Y. / Dalluge, J.J. / Ronning, D.R. / Aldrich, C.C.
History
DepositionAug 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: 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 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
C: Homoserine O-acetyltransferase
D: Homoserine O-acetyltransferase
E: Homoserine O-acetyltransferase
F: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,73116
Polymers231,7216
Non-polymers5,01010
Water6,648369
1
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0847
Polymers77,2402
Non-polymers1,8435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-35 kcal/mol
Surface area25780 Å2
MethodPISA
2
C: Homoserine O-acetyltransferase
D: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7754
Polymers77,2402
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-16 kcal/mol
Surface area26110 Å2
MethodPISA
3
E: Homoserine O-acetyltransferase
F: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8715
Polymers77,2402
Non-polymers1,6313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-30 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.018, 160.991, 161.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Homoserine O-acetyltransferase / HAT / Homoserine transacetylase / HTA


Mass: 38620.180 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: metXA, metA / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJY9, homoserine O-acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium tartrate dibasic, 18% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12712 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 75155 / % possible obs: 98.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.083 / Rrim(I) all: 0.224 / Χ2: 1.337 / Net I/σ(I): 5.1 / Num. measured all: 465929
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.54-2.584.30.78835300.5870.3790.8810.49293.8
2.58-2.634.90.75736500.6890.3350.8340.49696.1
2.63-2.685.90.68936750.8060.2740.7450.51597.7
2.68-2.746.20.59737280.8470.2370.6460.58298.5
2.74-2.86.30.54737350.8630.2150.590.698.9
2.8-2.866.40.47537620.8990.1860.5120.65899
2.86-2.936.40.42437300.9120.1660.4570.70598.9
2.93-3.016.50.3837390.9210.150.410.81398.6
3.01-3.16.50.3437590.9360.1340.3660.86498.8
3.1-3.26.50.29637490.9460.1160.3190.93398.6
3.2-3.316.50.25837750.9530.1030.2791.16198.5
3.31-3.456.50.22137590.960.0890.241.36998.6
3.45-3.66.60.19737460.9710.0790.2131.68898.5
3.6-3.796.60.17237830.9760.0690.1861.97198.8
3.79-4.036.30.1537820.9820.0610.1632.2398.6
4.03-4.346.20.13237730.9830.0550.1442.35398.1
4.34-4.785.50.11237040.9860.050.1232.1895.9
4.78-5.4760.10237910.990.0430.1111.98197.3
5.47-6.897.10.09439210.9840.0360.1011.90699.8
6.89-506.70.06240640.9970.0240.0672.44898.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PUX

6pux


Resolution: 2.67→39.06 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1836 2.67 %
Rwork0.179 66833 -
obs0.1805 68669 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.66 Å2 / Biso mean: 25.2626 Å2 / Biso min: 5.29 Å2
Refinement stepCycle: final / Resolution: 2.67→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16210 0 312 369 16891
Biso mean--41.63 22.13 -
Num. residues----2195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.740.32371380.23575054519298
2.74-2.820.28691380.21615075521399
2.82-2.910.29561440.22265107525199
2.91-3.020.27961430.21455081522499
3.02-3.140.27841390.20785101524099
3.14-3.280.25631410.20535122526399
3.28-3.450.281370.1935109524699
3.45-3.670.24871390.18025136527599
3.67-3.950.23171390.16035141528099
3.95-4.350.20071440.15315150529498
4.35-4.980.18811360.14655034517096
4.98-6.270.22291460.15915263540999
6.27-39.060.17391520.15335460561299

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