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- PDB-6pux: Homoserine transacetylase MetX from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6pux
TitleHomoserine transacetylase MetX from Mycobacterium tuberculosis
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / methionine biosynthesis / HOMOSERINE O-ACETYLTRANSFERASE / HOMOSERINE O-TRANSACETYLASE / HTA / MetX / Rv3341
Function / homology
Function and homology information


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, 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 tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsChaton, C.T. / 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
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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 1.4Oct 11, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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 / _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)77,73921
Polymers76,5302
Non-polymers1,20919
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-197 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.460, 86.680, 208.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38264.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: metXA, metA, Rv3341, MTV016.41 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: P9WJY9, homoserine O-acetyltransferase

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Non-polymers , 5 types, 533 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.16 % / Description: broken prizm
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, 1.8 M Magnesium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 28, 2019
Details: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR: LIQUID NITROGEN COOLED; SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.713 Å / Num. obs: 68862 / % possible obs: 99.8 % / Redundancy: 7.373 % / Biso Wilson estimate: 31.305 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.154 / Χ2: 1.018 / Net I/σ(I): 11.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.957.3451.3611.2936569499349790.6721.46599.7
1.95-26.7691.0481.6932973489848710.7441.13599.4
2-2.067.3360.8612.235426483148290.8370.927100
2.06-2.127.8060.7172.8635713457845750.8780.76899.9
2.12-2.197.7220.5433.834820450945090.9320.582100
2.19-2.277.6320.4564.6433458438843840.9480.48999.9
2.27-2.367.5130.3945.4231727422542230.9560.424100
2.36-2.457.4440.3296.4929970403340260.970.35499.8
2.45-2.567.4560.3017.4328921388238790.9760.32499.9
2.56-2.697.2580.2588.7227168374937430.9790.27899.8
2.69-2.836.7210.20510.3323841356335470.9850.22299.6
2.83-37.1940.15813.5224373339533880.9920.1799.8
3-3.217.7770.11918.1724785319031870.9950.12899.9
3.21-3.477.720.08922.7822783295629510.9970.09599.8
3.47-3.87.5380.0727.5220670274327420.9980.075100
3.8-4.257.4350.05531.9718566250224970.9980.0699.8
4.25-4.917.1720.04933.1915980223222280.9980.05399.8
4.91-6.016.5240.0483112415191119030.9980.05299.6
6.01-8.57.6370.04335.4811493150515050.9990.046100
8.5-44.7136.7830.03340.5960789028960.9990.03599.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSVERSION Mar 15, 2019data reduction
XSCALEVERSION Mar 15, 2019data scaling
PHASER2.8.3phasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W8P

5w8p


Resolution: 1.9→44.713 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.1 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 6562 5.03 %
Rwork0.1683 --
obs0.17 68843 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.27 Å2 / Biso mean: 36.1809 Å2 / Biso min: 16.36 Å2
Refinement stepCycle: final / Resolution: 1.9→44.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 68 514 5966
Biso mean--68.9 38.96 -
Num. residues----731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.31472160.3149406199
1.9216-1.94420.32891940.29974182100
1.9442-1.96790.3211920.2917417199
1.9679-1.99280.29362040.27514110100
1.9928-2.0190.33572170.2743412099
2.019-2.04670.30132600.2564110100
2.0467-2.07590.29122130.24354150100
2.0759-2.10690.27031830.24054153100
2.1069-2.13980.27091740.21324220100
2.1398-2.17490.23472430.20534113100
2.1749-2.21240.21742230.19864111100
2.2124-2.25260.19132130.19194201100
2.2526-2.2960.23962550.18534096100
2.296-2.34280.22451970.18424181100
2.3428-2.39380.18782020.17774103100
2.3938-2.44940.21222560.17324088100
2.4494-2.51070.20772470.17494139100
2.5107-2.57860.25312360.17364113100
2.5786-2.65440.20462200.1733412099
2.6544-2.74010.24331950.1622414599
2.7401-2.8380.18822070.1565411499
2.838-2.95160.21412180.1552414299
2.9516-3.08590.1972200.15114121100
3.0859-3.24860.16252140.14674140100
3.2486-3.45210.18962070.13624161100
3.4521-3.71850.15742220.12564152100
3.7185-4.09240.14792410.1184106100
4.0924-4.68410.15322340.11934140100
4.6841-5.89930.17672000.1468415099
5.8993-44.7130.19682590.1984085100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30780.11540.31420.74220.32931.31070.03380.0462-0.0825-0.05470.0117-0.03190.19870.0748-0.0480.22710.01630.00790.1786-0.02030.21815.03428.393851.2787
21.8686-1.5046-0.0951.91980.74180.7767-0.089-0.1372-0.18540.08320.05440.30950.148-0.16750.05890.1986-0.03230.00560.25330.01330.2401-5.94318.101676.9973
30.4284-0.26970.14190.6220.50681.0494-0.00150.0413-0.0241-0.007-0.0007-0.0545-0.01220.00120.00420.1781-0.01630.00910.187-0.00890.20875.656620.81258.7256
41.2480.1957-0.23451.26420.03912.1760.07230.05770.048-0.2708-0.04890.1634-0.1319-0.2246-0.0280.27820.0229-0.01930.23860.00060.2616-5.659926.110850.0695
52.79331.32630.5622.02520.18371.1202-0.0485-0.21160.01630.271-0.0198-0.197-0.14280.10510.08150.30830.0118-0.03690.28960.01260.26955.624729.4904107.358
61.0327-0.02530.21361.0565-0.4970.772-0.0357-0.09680.09960.2303-0.0452-0.2665-0.13990.14760.04740.2476-0.0286-0.05050.25550.00190.268613.789239.912697.7447
70.78490.16690.01161.4939-0.59060.935-0.0355-0.1484-0.03780.0840.0831-0.03260.01950.0237-0.05240.19790.0077-0.0170.25620.00460.1988.147525.4674101.3309
81.52161.09951.10671.4137-0.06632.32290.0275-0.16770.03720.3220.06910.0442-0.1732-0.0285-0.06010.2890.02060.03460.2601-0.01560.22650.582736.1251103.5106
91.64920.45150.27571.73740.05670.6772-0.0347-0.04540.08140.20530.05590.1036-0.151-0.1222-0.01470.21610.03770.02060.23970.01880.2132-1.993338.924992.6163
100.65350.1053-0.47271.2039-0.09931.0807-0.0654-0.0422-0.0770.06650.0194-0.21650.07070.19920.03790.19190.0119-0.01880.22780.00020.234912.875219.241877.8845
110.0817-0.0868-0.31850.28140.12091.4824-0.0498-0.074-0.08930.06450.0361-0.140.09850.33230.01280.17670.0109-0.01360.29070.00490.248912.949722.117484.0994
120.42160.1251-0.05230.6016-0.23020.7559-0.0572-0.05610.0484-0.03410.10560.1425-0.0577-0.0991-0.05290.1830.02080.01530.24860.02410.2329-6.50438.415884.0497
131.895-0.135-0.38481.49540.50652.0689-0.01030.01860.214-0.02210.0655-0.1139-0.36460.1522-0.07250.2525-0.00390.00310.23360.0130.26185.880746.092183.3061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 219 )A7 - 219
2X-RAY DIFFRACTION2chain 'A' and (resid 220 through 260 )A220 - 260
3X-RAY DIFFRACTION3chain 'A' and (resid 261 through 334 )A261 - 334
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 372 )A335 - 372
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 35 )B8 - 35
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 92 )B36 - 92
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 130 )B93 - 130
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 151 )B131 - 151
9X-RAY DIFFRACTION9chain 'B' and (resid 152 through 187 )B152 - 187
10X-RAY DIFFRACTION10chain 'B' and (resid 188 through 260 )B188 - 260
11X-RAY DIFFRACTION11chain 'B' and (resid 261 through 290 )B261 - 290
12X-RAY DIFFRACTION12chain 'B' and (resid 291 through 334 )B291 - 334
13X-RAY DIFFRACTION13chain 'B' and (resid 335 through 372 )B335 - 372

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