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- PDB-4qfw: Crystal structure of acyl-CoA thioesterase tesB from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 4qfw
TitleCrystal structure of acyl-CoA thioesterase tesB from Yersinia pestis
ComponentsAcyl-CoA thioesterase II
KeywordsHYDROLASE / Double-HotDog / 4HBT-like / thioesterase / acyl-CoA thioesterase
Function / homology
Function and homology information


acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol
Similarity search - Function
Acyl-CoA thioesterase / Acyl-CoA thioesterase II domain / Acyl-CoA thioesterase / Acyl-CoA thioesterase, double hotdog domain / Acyl-CoA thioesterase, double hotdog domain / : / Acyl-CoA thioesterase N-terminal domain / Porin / HotDog domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Acyl-CoA thioesterase II / Acyl-CoA thioesterase II
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSwarbrick, C.M.D. / Forwood, J.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization of the acyl-CoA thioesterase TesB from Yersinia pestis.
Authors: Swarbrick, C.M. / Patterson, E.I. / Forwood, J.K.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJun 4, 2014ID: 4GWH
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA thioesterase II
B: Acyl-CoA thioesterase II
C: Acyl-CoA thioesterase II
D: Acyl-CoA thioesterase II


Theoretical massNumber of molelcules
Total (without water)130,8124
Polymers130,8124
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-31 kcal/mol
Surface area41740 Å2
MethodPISA
2
A: Acyl-CoA thioesterase II
B: Acyl-CoA thioesterase II


Theoretical massNumber of molelcules
Total (without water)65,4062
Polymers65,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-10 kcal/mol
Surface area21710 Å2
MethodPISA
3
C: Acyl-CoA thioesterase II
D: Acyl-CoA thioesterase II


Theoretical massNumber of molelcules
Total (without water)65,4062
Polymers65,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-12 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.230, 171.620, 73.700
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsConfirmed using size exclusion chromatography, analytical ultracentrifugation and small angle X-Ray scattering the tetramer present in the asymmetric unit is the biological assembly.

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Components

#1: Protein
Acyl-CoA thioesterase II


Mass: 32702.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: tesB, tesB y1043 YP_0790, y1043, YPO3141, YP_0790 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 pLysS
References: UniProt: Q0WCE2, UniProt: A0A3N4BCC7*PLUS, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 235mM sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→54.29 Å / Num. all: 446767 / Num. obs: 75550 / % possible obs: 93.68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.04 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4191 / % possible all: 87.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1C8U

1c8u


Resolution: 2→24.29 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.272 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26813 3827 5.1 %RANDOM
Rwork0.22071 ---
obs0.22313 71671 93.68 %-
all-71671 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8460 0 0 207 8667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198684
X-RAY DIFFRACTIONr_bond_other_d0.0060.028071
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.94711761
X-RAY DIFFRACTIONr_angle_other_deg0.875318542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90751048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36623.571448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.132151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.361568
X-RAY DIFFRACTIONr_chiral_restr0.1050.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022147
X-RAY DIFFRACTIONr_mcbond_it2.6042.8124228
X-RAY DIFFRACTIONr_mcbond_other2.6042.8114227
X-RAY DIFFRACTIONr_mcangle_it3.8074.1975264
X-RAY DIFFRACTIONr_mcangle_other3.8074.1985265
X-RAY DIFFRACTIONr_scbond_it2.8923.1214456
X-RAY DIFFRACTIONr_scbond_other2.8923.1224457
X-RAY DIFFRACTIONr_scangle_other4.3734.5616498
X-RAY DIFFRACTIONr_long_range_B_refined6.18422.5419549
X-RAY DIFFRACTIONr_long_range_B_other6.18822.5399481
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 265 -
Rwork0.29 4926 -
obs-4926 87.1 %

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