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- PDB-6iog: Crystal structure of Homoserine O-acetyltransferase from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 6iog
TitleCrystal structure of Homoserine O-acetyltransferase from Mycobacterium smegmatis ATCC 19420
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


homoserine metabolic process / homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / methionine biosynthetic process / cytoplasm
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Homoserine O-acetyltransferase / Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure and biochemical characterization of O-acetylhomoserine acetyltransferase from Mycobacterium smegmatis ATCC 19420.
Authors: Sagong, H.Y. / Hong, J. / Kim, K.J.
History
DepositionOct 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Assembly

Deposited unit
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0443
Polymers78,9522
Non-polymers921
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-22 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.357, 96.246, 140.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39475.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: metX_1, metXA, ERS451418_01697 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3)
References: UniProt: A0A0D6HE46, UniProt: A0QSZ0*PLUS, homoserine O-acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 32 % (v/v) polyethylene glycol (PEG) 400, 0.1 M Sodium acetate/acetic acid pH 5.5, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 112835 / % possible obs: 97.4 % / Redundancy: 5.9 % / Rpim(I) all: 0.034 / Net I/σ(I): 39.72
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.61 / Num. unique obs: 5476 / Rpim(I) all: 0.152 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVM

3vvm


Resolution: 1.55→29.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.288 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 5569 4.9 %RANDOM
Rwork0.1715 ---
obs0.1727 107228 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.56 Å2 / Biso mean: 18.384 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.07 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.55→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 6 577 6065
Biso mean--36.34 26.71 -
Num. residues----740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135618
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175152
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6387670
X-RAY DIFFRACTIONr_angle_other_deg1.5721.57511890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.68921.153295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07915814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.391549
X-RAY DIFFRACTIONr_chiral_restr0.090.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021189
LS refinement shellResolution: 1.546→1.586 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 369 -
Rwork0.219 7330 -
all-7699 -
obs--90.42 %

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