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- PDB-6fw5: TesA a major thioesterase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6fw5
TitleTesA a major thioesterase from Mycobacterium tuberculosis
ComponentsProbable thioesterase TesA
KeywordsHYDROLASE / Thioesterase / Mycobacterium tuberculosis
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Thioester hydrolases / biosynthetic process / hydrolase activity, acting on ester bonds / : / lipid metabolic process
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
PHOSPHATE ION / Thioesterase TesA
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 5, 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 1.2Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_site / struct_site_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable thioesterase TesA
B: Probable thioesterase TesA
C: Probable thioesterase TesA
D: Probable thioesterase TesA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1238
Polymers116,7434
Non-polymers3804
Water1,44180
1
A: Probable thioesterase TesA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2812
Polymers29,1861
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable thioesterase TesA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2812
Polymers29,1861
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Probable thioesterase TesA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2812
Polymers29,1861
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Probable thioesterase TesA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2812
Polymers29,1861
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.580, 224.650, 226.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
Probable thioesterase TesA


Mass: 29185.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: tesA, MT2998 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WQD4, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 45% PEG 600, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.75→43.87 Å / Num. obs: 24307 / % possible obs: 93.1 % / Redundancy: 7.2 % / Biso Wilson estimate: 145.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10
Reflection shellResolution: 2.75→2.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4055 / CC1/2: 0.753 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→39.89 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.411
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1216 5 %RANDOM
Rwork0.271 ---
obs0.272 24306 93.1 %-
Displacement parametersBiso mean: 133.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.1816 Å20 Å20 Å2
2--5.8183 Å20 Å2
3----5.6367 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: 1 / Resolution: 2.75→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 20 80 6866
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116985HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.239525HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2212SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1193HARMONIC5
X-RAY DIFFRACTIONt_it6985HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion23.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion932SEMIHARMONIC5
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_contact8324SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.87 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3118 152 5.02 %
Rwork0.2933 2874 -
all0.2942 3026 -
obs--96.19 %
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)
11.1516-0.59240.73310.8333-0.16891.69170.0017-0.0199-0.0265-0.08840.02640.0279-0.02020.0091-0.0281-0.11110.0303-0.05440.02620.01760.0161-43.500171.2773-16.718
20.0723-0.22350.07852.18410.63020.6769-0.009-0.0456-0.026-0.01680.00430.03360.0067-0.01270.0047-0.1030.0465-0.0487-0.0428-0.08820.0543-33.526133.9504-16.6032
300.0498-0.96141.77060.6060.78410.0059-0.0268-0.0024-0.055-0.0023-0.0326-0.0242-0.0157-0.00360.0594-0.02990.0732-0.0886-0.00970.006-24.700613.7677-39.9609
400.2104-0.98071.90270.7231.0612-0.0041-0.0487-0.0317-0.05430.0301-0.0194-0.0234-0.01-0.0260.0856-0.03410.1092-0.047-0.0069-0.0675-64.922420.3277-39.2455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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