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Basic information

Entry
Database: PDB / ID: 3kuw
TitleStructural basis of the activity ans substrate specificity of the fluoroacetyl-CoA thioesterase FlK - T42S mutant in complex with Fluoro-acetate
ComponentsFluoroacetyl coenzyme A thioesterase
KeywordsHYDROLASE / fluoroacetyl-CoA thioesterase FlK / thioesterase / hot-dog folding
Function / homology
Function and homology information


fluoroacetyl-CoA thioesterase / acyl-CoA hydrolase activity / protein homodimerization activity
Similarity search - Function
Fluoroacetyl-CoA thioesterase / Fluoroacetyl-CoA-specific thioesterase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
fluoroacetic acid / Fluoroacetyl-CoA thioesterase
Similarity search - Component
Biological speciesStreptomyces Cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsDias, M.V.B. / Huang, F. / Chirgadze, D.Y. / Tosin, M. / Spiteller, D. / Valentine, E.F. / Leadlay, P.F. / Spencer, J.B. / Blundell, T.L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK.
Authors: Dias, M.V. / Huang, F. / Chirgadze, D.Y. / Tosin, M. / Spiteller, D. / Dry, E.F. / Leadlay, P.F. / Spencer, J.B. / Blundell, T.L.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluoroacetyl coenzyme A thioesterase
B: Fluoroacetyl coenzyme A thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8436
Polymers30,5312
Non-polymers3124
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-19 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.504, 92.896, 49.594
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fluoroacetyl coenzyme A thioesterase


Mass: 15265.410 Da / Num. of mol.: 2 / Fragment: FlK / Mutation: T42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces Cattleya (bacteria) / Strain: Streptomyces Cattleya / Gene: flK, fluoroacetyl-CoA thioesterase FlK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EMV2, Hydrolases
#2: Chemical
ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3FO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: This-HCl, Fluoroacetate, PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: 2008 / Details: mirrors
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→48.68 Å / Num. all: 21816 / Num. obs: 21719 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→2 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementStarting model: PDB entry 1HNN

1hnn


Resolution: 1.9→38.45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.469 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.166 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25572 1107 5.1 %RANDOM
Rwork0.18493 ---
all0.19 21816 --
obs0.18866 20484 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 20 284 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9462906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32222.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12915319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8521516
X-RAY DIFFRACTIONr_chiral_restr0.1490.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211651
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1051.51344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.89422172
X-RAY DIFFRACTIONr_scbond_it3.1323791
X-RAY DIFFRACTIONr_scangle_it4.9244.5734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 79 -
Rwork0.347 1459 -
obs--96.67 %

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