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- PDB-3kv8: Structural basis of the activity and substrate specificity of the... -

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Basic information

Entry
Database: PDB / ID: 3kv8
TitleStructural basis of the activity and substrate specificity of the fluoroacetyl-CoA thioesterase FlK - Wild type FlK in complex with fluoro-acetate
ComponentsFluoroacetyl-CoA thioesterase FlK
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: 1.85 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 29, 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 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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-CoA thioesterase FlK
B: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0278
Polymers30,5592
Non-polymers4686
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-13 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.430, 92.990, 50.090
Angle α, β, γ (deg.)90.00, 101.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fluoroacetyl-CoA thioesterase FlK


Mass: 15279.436 Da / Num. of mol.: 2 / Fragment: FlK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces Cattleya (bacteria) / Gene: flK, fluoroacetyl-CoA thioesterase FlK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1EMV2, Hydrolases
#2: Chemical
ChemComp-FAH / fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3FO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris HCl PEG4000 Sodium Fluoroacetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: 2008 / Details: mirrors
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30.59 Å / Num. all: 24031 / Num. obs: 23674 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.85→1.95 Å / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementStarting model: PDB entry 1HNN

1hnn


Resolution: 1.85→28.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.825 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.134 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1215 5.1 %RANDOM
Rwork0.16906 ---
all0.179 24031 --
obs0.17199 22459 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 30 218 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9512923
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25621.75891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8141519
X-RAY DIFFRACTIONr_chiral_restr0.1590.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211663
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_it1.3081.51348
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.222178
X-RAY DIFFRACTIONr_scbond_it3.6443804
X-RAY DIFFRACTIONr_scangle_it5.8824.5745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 81 -
Rwork0.225 1575 -
obs--94.36 %

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