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- PDB-3p3f: Crystal structure of the F36A mutant of the fluoroacetyl-CoA-spec... -

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Basic information

Entry
Database: PDB / ID: 3p3f
TitleCrystal structure of the F36A mutant of the fluoroacetyl-CoA-specific thioesterase FlK
ComponentsFluoroacetyl coenzyme A thioesterase
KeywordsHYDROLASE / hot dog-fold / thioesterase
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
Fluoroacetyl-CoA thioesterase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWeeks, A.M. / Coyle, S.M. / Jinek, M. / Doudna, J.A. / Chang, M.C.Y.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity.
Authors: Weeks, A.M. / Coyle, S.M. / Jinek, M. / Doudna, J.A. / Chang, M.C.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Fluoroacetyl coenzyme A thioesterase
B: Fluoroacetyl coenzyme A thioesterase
C: Fluoroacetyl coenzyme A thioesterase
D: Fluoroacetyl coenzyme A thioesterase
E: Fluoroacetyl coenzyme A thioesterase
F: Fluoroacetyl coenzyme A thioesterase


Theoretical massNumber of molelcules
Total (without water)92,9386
Polymers92,9386
Non-polymers00
Water10,070559
1
A: Fluoroacetyl coenzyme A thioesterase
B: Fluoroacetyl coenzyme A thioesterase


Theoretical massNumber of molelcules
Total (without water)30,9792
Polymers30,9792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-28 kcal/mol
Surface area12390 Å2
MethodPISA
2
C: Fluoroacetyl coenzyme A thioesterase
D: Fluoroacetyl coenzyme A thioesterase


Theoretical massNumber of molelcules
Total (without water)30,9792
Polymers30,9792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-27 kcal/mol
Surface area12210 Å2
MethodPISA
3
E: Fluoroacetyl coenzyme A thioesterase
F: Fluoroacetyl coenzyme A thioesterase


Theoretical massNumber of molelcules
Total (without water)30,9792
Polymers30,9792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-30 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.380, 88.820, 71.080
Angle α, β, γ (deg.)90.00, 117.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-149-

HOH

21E-422-

HOH

31E-431-

HOH

41E-435-

HOH

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Components

#1: Protein
Fluoroacetyl coenzyme A thioesterase


Mass: 15489.625 Da / Num. of mol.: 6 / Mutation: F36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: flK / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EMV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Tris-HCl, pH 7.6 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2010
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.3→19.75 Å / Num. all: 34432 / Num. obs: 34432 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.48 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.75 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1722 5 %
Rwork0.2203 --
obs0.2216 34432 99.12 %
all-34432 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.131 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8739 Å2-0 Å23.5165 Å2
2---2.4418 Å20 Å2
3----11.7955 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 0 559 6649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176258
X-RAY DIFFRACTIONf_angle_d1.4668511
X-RAY DIFFRACTIONf_dihedral_angle_d18.5552247
X-RAY DIFFRACTIONf_chiral_restr0.109948
X-RAY DIFFRACTIONf_plane_restr0.0091107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2954-2.36280.28381390.26322632X-RAY DIFFRACTION96
2.3628-2.43890.29081420.24542705X-RAY DIFFRACTION99
2.4389-2.52590.30241430.24582715X-RAY DIFFRACTION99
2.5259-2.62690.25821420.24272699X-RAY DIFFRACTION99
2.6269-2.74610.26271430.23542723X-RAY DIFFRACTION99
2.7461-2.89050.29921430.23592723X-RAY DIFFRACTION99
2.8905-3.07090.24721450.2152737X-RAY DIFFRACTION99
3.0709-3.3070.22851430.20472717X-RAY DIFFRACTION100
3.307-3.6380.20191440.1882736X-RAY DIFFRACTION100
3.638-4.16010.20131460.18412776X-RAY DIFFRACTION100
4.1601-5.22520.23791440.18622745X-RAY DIFFRACTION99
5.2252-19.75480.21431480.23152802X-RAY DIFFRACTION100

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