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

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Basic information

Entry
Database: PDB / ID: 3kvu
TitleStructural basis of the activity and substrate specificity of the fluoroacetyl-CoA FlK - T42S mutant in complex with Acetyl-CoA
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
ACETYL COENZYME *A / Fluoroacetyl-CoA thioesterase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 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 1.5Nov 27, 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
C: Fluoroacetyl-CoA thioesterase FlK
D: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4907
Polymers61,0624
Non-polymers2,4293
Water6,431357
1
A: Fluoroacetyl-CoA thioesterase FlK
B: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1504
Polymers30,5312
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-25 kcal/mol
Surface area11380 Å2
MethodPISA
2
C: Fluoroacetyl-CoA thioesterase FlK
D: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3403
Polymers30,5312
Non-polymers8101
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-28 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.980, 55.970, 96.410
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fluoroacetyl-CoA thioesterase FlK


Mass: 15265.410 Da / Num. of mol.: 4 / Fragment: FlK / Mutation: T42S
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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 1.97 Å3/Da / Density % sol: 37.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris HCl peg 4000 acetyl-CoA, 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: X06DA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: 2008 / Details: mirrors
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→34.9 Å / Num. all: 32373 / Num. obs: 32361 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.11 Å / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementStarting model: PDB entry 1HNN

1hnn


Resolution: 2→31.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29467 1631 5 %RANDOM
Rwork0.21574 ---
obs0.21981 30715 99.95 %-
all-32373 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.01 Å2
2--0.05 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 88 357 4539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0214307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9911.9685874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4865528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57921.977177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26515641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.791535
X-RAY DIFFRACTIONr_chiral_restr0.2680.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2580.22058
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.22846
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.2145
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3790.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4771.52656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34324301
X-RAY DIFFRACTIONr_scbond_it3.68831651
X-RAY DIFFRACTIONr_scangle_it5.5794.51564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 118 -
Rwork0.269 2257 -
obs--100 %

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