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

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Basic information

Entry
Database: PDB / ID: 3kvz
TitleStructural basis of the activity and substrate specificity of the fluoroacetyl-CoA thiesterase FlK - wild type FlK in complex with FAcCPan
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
Chem-ENV / Fluoroacetyl-CoA thioesterase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
E: Fluoroacetyl-CoA thioesterase FlK
F: Fluoroacetyl-CoA thioesterase FlK
G: Fluoroacetyl-CoA thioesterase FlK
H: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,87610
Polymers122,2358
Non-polymers6412
Water10,287571
1
A: Fluoroacetyl-CoA thioesterase FlK
B: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8793
Polymers30,5592
Non-polymers3201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-29 kcal/mol
Surface area11650 Å2
MethodPISA
2
C: Fluoroacetyl-CoA thioesterase FlK
D: Fluoroacetyl-CoA thioesterase FlK


Theoretical massNumber of molelcules
Total (without water)30,5592
Polymers30,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-29 kcal/mol
Surface area11800 Å2
MethodPISA
3
E: Fluoroacetyl-CoA thioesterase FlK
F: Fluoroacetyl-CoA thioesterase FlK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8793
Polymers30,5592
Non-polymers3201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area11750 Å2
MethodPISA
4
G: Fluoroacetyl-CoA thioesterase FlK
H: Fluoroacetyl-CoA thioesterase FlK


Theoretical massNumber of molelcules
Total (without water)30,5592
Polymers30,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-30 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.500, 70.890, 102.880
Angle α, β, γ (deg.)90.00, 103.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fluoroacetyl-CoA thioesterase FlK


Mass: 15279.436 Da / Num. of mol.: 8 / 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-ENV / (2R)-N-{3-[(5-fluoro-4-oxopentyl)amino]-3-oxopropyl}-2,4-dihydroxy-3,3-dimethylbutanamide / Fluoroacetyl carba(dethia)-pantetheine


Mass: 320.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25FN2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: CHES tri-sodium citrate, pH 9.5, 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: 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 wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→33.98 Å / Num. all: 65288 / Num. obs: 62854 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.21 Å / % possible all: 96

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Processing

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

1hnn


Resolution: 2.1→33.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28164 3193 5.1 %RANDOM
Rwork0.20386 ---
obs0.20779 59640 96.28 %-
all-65288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8120 0 22 571 8713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228397
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.94711445
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.73751057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59622.105342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.473151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2171564
X-RAY DIFFRACTIONr_chiral_restr0.1180.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216462
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_it1.0211.55313
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75828597
X-RAY DIFFRACTIONr_scbond_it2.83733084
X-RAY DIFFRACTIONr_scangle_it4.3894.52848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 207 -
Rwork0.262 3947 -
obs--86.54 %

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