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- PDB-6fvj: TesA a major thioesterase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6fvj
TitleTesA a major thioesterase from Mycobacterium tuberculosis
ComponentsThioesterase
KeywordsHYDROLASE / TesA / thioesterase / Mycobacterium tuberculosis
Function / homology
Function and homology information


acetylesterase / palmitoyl-CoA hydrolase / symbiont-mediated perturbation of host innate immune response / acetylesterase activity / fatty acyl-CoA hydrolase activity / DIM/DIP cell wall layer assembly / Hydrolases; Acting on ester bonds; Thioester hydrolases / biosynthetic process / lipid biosynthetic process / ligase activity ...acetylesterase / palmitoyl-CoA hydrolase / symbiont-mediated perturbation of host innate immune response / acetylesterase activity / fatty acyl-CoA hydrolase activity / DIM/DIP cell wall layer assembly / Hydrolases; Acting on ester bonds; Thioester hydrolases / biosynthetic process / lipid biosynthetic process / ligase activity / hydrolase activity / plasma membrane
Similarity search - Function
Thioesterase type II, NRPS/PKS/S-FAS / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
hexadecyl dihydrogen phosphate / Thioesterase TesA / Thioesterase TesA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCambillau, C. / Nguyen, V.S. / Canaan, S.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Biochemical and Structural Characterization of TesA, a Major Thioesterase Required for Outer-Envelope Lipid Biosynthesis in Mycobacterium tuberculosis.
Authors: Nguyen, P.C. / Nguyen, V.S. / Martin, B.P. / Fourquet, P. / Camoin, L. / Spilling, C.D. / Cavalier, J.F. / Cambillau, C. / Canaan, S.
History
DepositionMar 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _struct_conn.conn_type_id / _struct_conn.id / _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.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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioesterase
B: Thioesterase
C: Thioesterase
D: Thioesterase
E: Thioesterase
F: Thioesterase
G: Thioesterase
H: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,56430
Polymers233,4868
Non-polymers4,07822
Water8,395466
1
A: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7855
Polymers29,1861
Non-polymers5994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7454
Polymers29,1861
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7855
Polymers29,1861
Non-polymers5994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7454
Polymers29,1861
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6263
Polymers29,1861
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7454
Polymers29,1861
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6263
Polymers29,1861
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5082
Polymers29,1861
Non-polymers3221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.070, 224.580, 222.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-478-

HOH

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Components

#1: Protein
Thioesterase / Thioesterase TesA


Mass: 29185.783 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mbtB_1, mbtB_2 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045JET3, UniProt: P9WQD5*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-E9H / hexadecyl dihydrogen phosphate


Mass: 322.420 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H35O4P
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 45% PEG 600, 0.1 M HEPES pH 7.5 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→43.83 Å / Num. obs: 61244 / % possible obs: 99.6 % / Redundancy: 13.4 % / Biso Wilson estimate: 85.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Net I/σ(I): 15.9
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.907 / Num. unique obs: 9662 / CC1/2: 0.773 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.83 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.89 / SU R Cruickshank DPI: 0.857 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.898 / SU Rfree Blow DPI: 0.313 / SU Rfree Cruickshank DPI: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3056 5 %RANDOM
Rwork0.236 ---
obs0.237 61125 99.8 %-
Displacement parametersBiso mean: 86.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.3945 Å20 Å20 Å2
2--1.5609 Å20 Å2
3----0.1664 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 2.6→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12928 0 157 466 13551
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913427HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0218267HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4310SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2252HARMONIC5
X-RAY DIFFRACTIONt_it13427HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion21.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1767SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15215SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2595 223 5 %
Rwork0.2596 4241 -
all0.2596 4464 -
obs--99.64 %
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)
11.8020.20150.12971.0694-1.26470.865-0.00340.0067-0.0015-0.0217-0.00550.0394-0.0068-0.00650.0089-0.0242-0.0196-0.0110.00530.14310.0069117.556263.931-202.305
21.99780.3904-0.24830.7835-0.62550.65840.00370.01360.0136-0.0308-0.0058-0.032-0.00470.0040.0021-0.0491-0.06250.0378-0.04030.07960.0622156.043263.163-204.258
31.80790.3494-0.92540.0055-0.46691.8434-0.00140.0099-0.00730.00170.00680.00730.02980.0038-0.0053-0.0536-0.03190.01910.09910.0883-0.0835106.391242.993-182.216
41.4311-0.6489-0.01470.4695-0.74131.0868-0.0034-0.0193-0.0348-0.0005-0.003-0.00750.02070.01560.0065-0.0075-0.02230.00820.0360.0595-0.0536145.003242.202-184.061
50.08311.0814-0.33361.8339-0.164400.00260.01440.01290.01080.0098-0.0028-0.0335-0.0003-0.0124-0.010.01370.0159-0.0640.0089-0.0206127.325298.143-204.278
60.5496-1.29770.32781.2059-0.30120-0.0017-0.02270.02030.0006-0.016-0.04820.00970.01160.0177-0.02740.05870.0549-0.09270.0470.0864126.288264.287-238.732
70.13650.18230.24560.25631.30150.29290.0006-0.009-0.01110.0291-0.0016-0.01180.0259-0.01030.0010.0262-0.0025-0.0378-0.0406-0.0351-0.0544134.405320.197-182.243
80.00890.08491.3380.1995-0.45300.0010.0003-0.0068-0.01170.00170.0038-0.00320.0128-0.0027-0.0023-0.0149-0.0892-0.04070.02340.011193.881319.307-183.568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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