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- PDB-5w8o: Homoserine transacetylase MetX from Mycobacterium hassiacum -

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Basic information

Entry
Database: PDB / ID: 5w8o
TitleHomoserine transacetylase MetX from Mycobacterium hassiacum
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / homoserine O-acetyltransferase / homoserine O-trans-acetylase / HTA / MetX / methionine biosynthesis / Rv3341
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsReed, R.W. / Rodriguez, E.S. / Li, J. / Korotkov, K.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: Sci Rep / Year: 2019
Title: Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site.
Authors: Chaton, C.T. / Rodriguez, E.S. / Reed, R.W. / Li, J. / Kenner, C.W. / Korotkov, K.V.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,9769
Polymers76,6782
Non-polymers2987
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-71 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.750, 93.230, 81.590
Angle α, β, γ (deg.)90.000, 94.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Homoserine O-acetyltransferase / Homoserine O-trans-acetylase / Homoserine transacetylase


Mass: 38338.906 Da / Num. of mol.: 2 / Fragment: UNP residues 13-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: metX, C731_1248 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: K5B926, homoserine O-acetyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.36 Å3/Da / Density % sol: 47.89 % / Description: rectangular prism
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.15M CALCIUM ACETATE, 21% PEG3350, 3% 1,6-DIAMINOHEXANE, 0.05M CHES PH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2017
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→47.584 Å / Num. obs: 118675 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.776 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Χ2: 1.048 / Net I/σ(I): 18.01 / Num. measured all: 448067 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.47-1.513.781.0131.4688630.6951.18399.1
1.51-1.553.7340.7681.985610.8380.89998.9
1.55-1.593.6930.6252.3582230.8630.73397.1
1.59-1.643.6740.495378540.8940.5896
1.64-1.73.8350.3893.9479000.9410.45399.3
1.7-1.763.8480.3244.9176070.9510.37799.2
1.76-1.823.7890.2376.4773650.9720.27798.8
1.82-1.93.6950.1718.6769250.9830.20197
1.9-1.983.7720.11912.0566530.990.13996.8
1.98-2.083.8870.08816.0465020.9950.10399.3
2.08-2.193.8440.06720.2761660.9960.07899.2
2.19-2.323.790.0525.6758560.9970.05999.1
2.32-2.483.6040.0429.3153060.9980.04796
2.48-2.683.950.03534.8851500.9990.0499.2
2.68-2.943.9110.02742.1947190.9990.03299.3
2.94-3.293.7590.02249.9542740.9990.02698.8
3.29-3.83.5620.01956.3336750.9990.02296.6
3.8-4.653.8910.01666.76321810.01899.5
4.65-6.573.6910.01564.76248510.01798.8
6.57-47.5843.8450.01371.84137310.01598.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.04 Å47.41 Å
Translation2.04 Å47.41 Å

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Processing

Software
NameVersionClassification
XSCALEVERSION Nov 1, 2016 BUILT=20161205data scaling
PHASER2.7.17phasing
PHENIXdev_2722refinement
PDB_EXTRACT3.22data extraction
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I1I

3i1i


Resolution: 1.47→47.584 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 5840 4.94 %RANDOM SELECTION
Rwork0.153 ---
obs0.1545 118621 95.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.46 Å2 / Biso mean: 28.3645 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: final / Resolution: 1.47→47.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 18 593 5737
Biso mean--39.5 36.73 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055264
X-RAY DIFFRACTIONf_angle_d0.7657173
X-RAY DIFFRACTIONf_chiral_restr0.067814
X-RAY DIFFRACTIONf_plane_restr0.005946
X-RAY DIFFRACTIONf_dihedral_angle_d14.9251876
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.48670.36993770.33827396777397
1.4867-1.50420.3363860.32657265765197
1.5042-1.52260.32593860.29787212759896
1.5226-1.54180.34554000.28827364776496
1.5418-1.56210.30763650.26657122748796
1.5621-1.58350.26923260.2577246757294
1.5835-1.60620.26853580.2436899725791
1.6062-1.63010.26613450.22387025737093
1.6301-1.65560.22353710.21117371774297
1.6556-1.68270.24663940.20487209760397
1.6827-1.71180.22363570.19917481783897
1.7118-1.74290.24473370.19217358769597
1.7429-1.77640.20943500.1847393774397
1.7764-1.81270.21453950.17677266766197
1.8127-1.85210.22074140.16197298771296
1.8521-1.89520.20343600.1537051741194
1.8952-1.94260.20464180.14766965738392
1.9426-1.99510.17114330.12967354778798
1.9951-2.05380.1924090.13457315772497
2.0538-2.12010.18024250.13327283770897
2.1201-2.19590.16513780.12877346772497
2.1959-2.28380.17223910.12257362775397
2.2838-2.38770.16774050.12477201760696
2.3877-2.51360.16234170.12316976739393
2.5136-2.67110.16233760.13047364774097
2.6711-2.87730.18313390.1327366770597
2.8773-3.16680.16953600.13417384774497
3.1668-3.62490.15773260.14447012733892
3.6249-4.56640.13593490.1327302765197
4.5664-47.60860.1753630.16997325768896

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