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- PDB-3p3i: Crystal structure of the F36A mutant of the fluoroacetyl-CoA-spec... -

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Basic information

Entry
Database: PDB / ID: 3p3i
TitleCrystal structure of the F36A mutant of the fluoroacetyl-CoA-specific thioesterase FlK in complex with fluoroacetate and CoA
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 / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / fluoroacetic acid / Fluoroacetyl-CoA thioesterase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,62910
Polymers92,9386
Non-polymers1,6914
Water4,882271
1
A: Fluoroacetyl coenzyme A thioesterase
B: Fluoroacetyl coenzyme A thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8254
Polymers30,9792
Non-polymers8462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-31 kcal/mol
Surface area12030 Å2
MethodPISA
2
C: Fluoroacetyl coenzyme A thioesterase
D: Fluoroacetyl coenzyme A thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8254
Polymers30,9792
Non-polymers8462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-27 kcal/mol
Surface area11630 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 area3910 Å2
ΔGint-30 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.556, 89.008, 71.202
Angle α, β, γ (deg.)90.00, 118.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-182-

HOH

21B-141-

HOH

31E-266-

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: Chemical ChemComp-FAH / fluoroacetic acid / Fluoroacetic acid


Mass: 78.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3FO2
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.22 %
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: 1.9→72.48 Å / Num. all: 48041 / Num. obs: 48041 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.95 Å

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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→72.48 Å / SU ML: 0.28 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 1938 4.03 %random
Rwork0.2179 ---
all0.2195 48041 --
obs0.2193 48041 91.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.701 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.0478 Å2-0 Å22.4297 Å2
2---6.4823 Å20 Å2
3----11.2962 Å2
Refinement stepCycle: LAST / Resolution: 2→72.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6053 0 28 271 6352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076246
X-RAY DIFFRACTIONf_angle_d1.0158491
X-RAY DIFFRACTIONf_dihedral_angle_d17.4332241
X-RAY DIFFRACTIONf_chiral_restr0.071944
X-RAY DIFFRACTIONf_plane_restr0.0061106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30791370.23513048X-RAY DIFFRACTION85
2.05-2.10540.25191260.22343074X-RAY DIFFRACTION86
2.1054-2.16740.26851260.22253150X-RAY DIFFRACTION88
2.1674-2.23740.24891220.22363228X-RAY DIFFRACTION89
2.2374-2.31730.26731460.22293235X-RAY DIFFRACTION90
2.3173-2.41010.26381250.22483230X-RAY DIFFRACTION90
2.4101-2.51980.2651360.22313298X-RAY DIFFRACTION91
2.5198-2.65270.2581400.23043294X-RAY DIFFRACTION92
2.6527-2.81890.27511480.22993339X-RAY DIFFRACTION93
2.8189-3.03650.24621480.21193385X-RAY DIFFRACTION94
3.0365-3.34210.24451420.21773433X-RAY DIFFRACTION95
3.3421-3.82570.24721440.2043445X-RAY DIFFRACTION95
3.8257-4.81980.22831400.19363433X-RAY DIFFRACTION94
4.8198-72.52710.22781580.2253511X-RAY DIFFRACTION95

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