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- PDB-8f2l: Crystal structure of Mycobacterium tuberculosis Homoserine transa... -

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Basic information

Entry
Database: PDB / ID: 8f2l
TitleCrystal structure of Mycobacterium tuberculosis Homoserine transacetylase in complex with L-Homoserine
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / Alpha beta hydrolase / L-homoserine / acetyl transferase / Methionine biosynthesis
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
L-HOMOSERINE / Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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)R21-AI151924 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
DepositionNov 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Homoserine O-acetyltransferase
A: Homoserine O-acetyltransferase
C: Homoserine O-acetyltransferase
D: Homoserine O-acetyltransferase
E: Homoserine O-acetyltransferase
F: Homoserine O-acetyltransferase
G: Homoserine O-acetyltransferase
H: Homoserine O-acetyltransferase
I: Homoserine O-acetyltransferase
J: Homoserine O-acetyltransferase
K: Homoserine O-acetyltransferase
L: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,24823
Polymers462,93812
Non-polymers1,31011
Water0
1
B: Homoserine O-acetyltransferase
A: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3954
Polymers77,1562
Non-polymers2382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-12 kcal/mol
Surface area26210 Å2
MethodPISA
2
C: Homoserine O-acetyltransferase
D: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3954
Polymers77,1562
Non-polymers2382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-13 kcal/mol
Surface area26180 Å2
MethodPISA
3
E: Homoserine O-acetyltransferase
F: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2753
Polymers77,1562
Non-polymers1191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-17 kcal/mol
Surface area26180 Å2
MethodPISA
4
G: Homoserine O-acetyltransferase
H: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3954
Polymers77,1562
Non-polymers2382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-12 kcal/mol
Surface area25710 Å2
MethodPISA
5
I: Homoserine O-acetyltransferase
J: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3954
Polymers77,1562
Non-polymers2382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-14 kcal/mol
Surface area26130 Å2
MethodPISA
6
K: Homoserine O-acetyltransferase
L: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3954
Polymers77,1562
Non-polymers2382
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-15 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.735, 161.735, 249.235
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 38578.145 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: metXA, metA, Rv3341, MTV016.41 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJY9, homoserine O-acetyltransferase
#2: Chemical
ChemComp-HSE / L-HOMOSERINE / Homoserine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium tartrate dibasic, 18% w/v polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 161132 / % possible obs: 99 % / Redundancy: 8.9 % / CC1/2: 0.949 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.078 / Rrim(I) all: 0.244 / Χ2: 2.97 / Net I/σ(I): 12.1
Reflection shellResolution: 2.89→2.94 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.882 / Num. unique obs: 15760 / CC1/2: 0.862 / Rpim(I) all: 0.301 / Rrim(I) all: 0.935

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.18.2-3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PUX

6pux


Resolution: 2.89→46.96 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 2010 1.25 %
Rwork0.1901 --
obs0.1907 160914 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32456 0 0 0 32456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133119
X-RAY DIFFRACTIONf_angle_d1.31345151
X-RAY DIFFRACTIONf_dihedral_angle_d11.6234806
X-RAY DIFFRACTIONf_chiral_restr0.0655113
X-RAY DIFFRACTIONf_plane_restr0.016029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.970.3841390.280211005X-RAY DIFFRACTION96
2.97-3.050.35381500.267911243X-RAY DIFFRACTION97
3.05-3.140.31111320.26211158X-RAY DIFFRACTION98
3.14-3.240.26421390.250611394X-RAY DIFFRACTION98
3.24-3.350.29231400.242611284X-RAY DIFFRACTION99
3.35-3.490.26651490.214411288X-RAY DIFFRACTION99
3.49-3.640.27031460.192611419X-RAY DIFFRACTION99
3.65-3.840.29011480.180711419X-RAY DIFFRACTION100
3.84-4.080.20851400.163111435X-RAY DIFFRACTION100
4.08-4.390.21811510.154711477X-RAY DIFFRACTION100
4.39-4.830.1841420.151611463X-RAY DIFFRACTION100
4.83-5.530.21191460.158911477X-RAY DIFFRACTION100
5.53-6.970.20291450.175711497X-RAY DIFFRACTION100
6.97-46.960.1891430.160211345X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -10.0673 Å / Origin y: 70.0164 Å / Origin z: -20.6238 Å
111213212223313233
T-0.5655 Å20.0125 Å2-0.0202 Å2-0.218 Å2-0.0222 Å2---0.0111 Å2
L0.2899 °2-0.0004 °2-0.0521 °2--0.1458 °20.0549 °2---0.1406 °2
S0.365 Å °0.0035 Å °-0.0134 Å °0.0799 Å °-0.2264 Å °0.0237 Å °-0.063 Å °0.0112 Å °0.1719 Å °
Refinement TLS groupSelection details: all

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