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- PDB-5w8p: Homoserine transacetylase MetX from Mycobacterium abscessus -

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Basic information

Entry
Database: PDB / ID: 5w8p
TitleHomoserine transacetylase MetX from Mycobacterium abscessus
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
: / PHOSPHATE ION / Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsRodriguez, E.S. / Reed, R.W. / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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

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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)78,90512
Polymers78,0732
Non-polymers83210
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-42 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.920, 197.920, 51.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 39036.582 Da / Num. of mol.: 2 / Fragment: UNP residues 13-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: metX, MAB_3688 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B1MG17, homoserine O-acetyltransferase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 3.48 Å3/Da / Density % sol: 64.7 % / Description: hexagonal prism
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.2M SODIUM DIHYDROGEN PHOSPHATE, 0.8M DIPOTASSIUM HYDROGEN PHOSPHATE, 0.2M LITHIUM SULFATE, 0.1 M CHES PH 9.0

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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 12, 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: 1.69→49.48 Å / Num. obs: 128103 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.647 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.137 / Χ2: 0.991 / Net I/σ(I): 8.7 / Num. measured all: 723417 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.735.7930.9631.7893480.6781.05798.9
1.73-1.785.7190.7862.291640.7440.86499.1
1.78-1.835.6050.6422.6789530.8150.70799.3
1.83-1.895.4120.5163.2586900.8650.5799.9
1.89-1.955.3840.3964.0683180.9050.43898.6
1.95-2.025.8890.3115.4581750.9490.34199.6
2.02-2.15.8410.2586.4978630.9610.28399.7
2.1-2.185.8090.2087.876170.9720.22999.5
2.18-2.285.7110.175972910.9770.19399.8
2.28-2.395.5060.1539.869730.9810.16999.9
2.39-2.525.4470.13710.5165590.9820.15298.5
2.52-2.675.9160.12911.9563270.9860.141100
2.67-2.865.80.11113.3759420.9890.122100
2.86-3.095.7510.09715.255130.990.107100
3.09-3.385.4390.08616.451060.990.09599.9
3.38-3.785.3160.07817.8145010.990.08797.5
3.78-4.365.7170.07719.7441090.9920.08599.7
4.36-5.345.6150.07619.8234630.9890.08499.6
5.34-7.565.1630.07218.3326450.9920.0897
7.56-49.485.7550.06721.3115460.9930.07398.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.55 Å81.31 Å
Translation6.55 Å81.31 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: 5W8O

5w8o


Resolution: 1.69→49.48 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.174 6439 5.03 %RANDOM SELECTION
Rwork0.1579 ---
obs0.1587 128098 97.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.48 Å2 / Biso mean: 23.9349 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 1.69→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 60 787 6335
Biso mean--46.43 34.78 -
Num. residues----739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065642
X-RAY DIFFRACTIONf_angle_d0.7897697
X-RAY DIFFRACTIONf_chiral_restr0.052851
X-RAY DIFFRACTIONf_plane_restr0.0051026
X-RAY DIFFRACTIONf_dihedral_angle_d9.8163272
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 (%)
1.69-1.70920.31724020.28437687808996
1.7092-1.72930.27514260.27167746817298
1.7293-1.75040.27054030.26197821822498
1.7504-1.77260.26044410.257718815997
1.7726-1.79590.25194240.24197752817698
1.7959-1.82050.23724140.22687839825398
1.8205-1.84650.23014410.21717737817898
1.8465-1.87410.2324970.20827739823698
1.8741-1.90330.22464040.20947653805796
1.9033-1.93450.21043750.19177742811798
1.9345-1.96790.19493830.18137881826498
1.9679-2.00370.21484580.17997776823499
2.0037-2.04220.18443610.17317902826398
2.0422-2.08390.19283810.16687845822698
2.0839-2.12920.17463850.15247869825498
2.1292-2.17880.15533770.1427831820899
2.1788-2.23320.1644110.14217828823998
2.2332-2.29360.17714340.1387878831299
2.2936-2.36110.16243360.13817907824398
2.3611-2.43730.17493870.14577751813896
2.4373-2.52440.1844240.14277848827299
2.5244-2.62550.18074670.14087832829999
2.6255-2.7450.17064370.14477856829399
2.745-2.88970.15044200.14317922834299
2.8897-3.07070.16173580.14457920827899
3.0707-3.30780.15263680.14677925829399
3.3078-3.64050.15024120.13947636804896
3.6405-4.16710.13314910.1297803829499
4.1671-5.24920.13894230.12857847827099
5.2492-49.50120.18044640.17867663812797

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