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- PDB-2f0x: Crystal structure and function of human thioesterase superfamily ... -

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Basic information

Entry
Database: PDB / ID: 2f0x
TitleCrystal structure and function of human thioesterase superfamily member 2(THEM2)
ComponentsThioesterase superfamily member 2
KeywordsHYDROLASE / hot dog fold
Function / homology
Function and homology information


palmitoyl-CoA hydrolase / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / Hydrolases; Acting on ester bonds; Thioester hydrolases / negative regulation of cold-induced thermogenesis / lipid metabolic process / spindle / protein homotetramerization / mitochondrial matrix / nucleus ...palmitoyl-CoA hydrolase / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / Hydrolases; Acting on ester bonds; Thioester hydrolases / negative regulation of cold-induced thermogenesis / lipid metabolic process / spindle / protein homotetramerization / mitochondrial matrix / nucleus / metal ion binding / cytosol
Similarity search - Function
Acyl-coenzyme A thioesterase 13 / Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Acyl-coenzyme A thioesterase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCheng, Z. / Song, F. / Shan, X. / Wang, Y. / Wei, Z. / Gong, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of human thioesterase superfamily member 2
Authors: Cheng, Z. / Song, F. / Shan, X. / Wei, Z. / Wang, Y. / Dunaway-Mariano, D. / Gong, W.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioesterase superfamily member 2
B: Thioesterase superfamily member 2
C: Thioesterase superfamily member 2
D: Thioesterase superfamily member 2
E: Thioesterase superfamily member 2
F: Thioesterase superfamily member 2
G: Thioesterase superfamily member 2
H: Thioesterase superfamily member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,96928
Polymers131,0478
Non-polymers1,92120
Water8,035446
1
A: Thioesterase superfamily member 2
B: Thioesterase superfamily member 2
C: Thioesterase superfamily member 2
D: Thioesterase superfamily member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,58015
Polymers65,5244
Non-polymers1,05711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-210 kcal/mol
Surface area19560 Å2
MethodPISA
2
E: Thioesterase superfamily member 2
F: Thioesterase superfamily member 2
G: Thioesterase superfamily member 2
H: Thioesterase superfamily member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,38813
Polymers65,5244
Non-polymers8659
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-192 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.937, 122.076, 90.977
Angle α, β, γ (deg.)90.00, 123.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thioesterase superfamily member 2


Mass: 16380.914 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NPJ3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M (NH4)2So4, 14-16% PEG2000, 0.1M NaAc-HAc pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11931
21
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.95, 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.9791
ReflectionRedundancy: 7.8 % / Number: 41105 / Rmerge(I) obs: 0.113 / Χ2: 1.256 / D res high: 2.5 Å / D res low: 50 Å / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.52.5610010.3620.8267.7
2.562.6210010.30.8757.8
2.622.6910010.2630.8867.8
2.692.7710010.2290.987.8
2.772.8610010.2241.0227.8
2.862.9610010.1921.0587.8
2.963.0810010.1681.217.8
3.083.2210010.1381.3647.8
3.223.3910010.121.457.8
3.393.6110010.1031.5347.8
3.613.8810010.0931.4387.8
3.884.2710010.0861.5747.8
4.274.8910010.0831.567.8
4.896.1610010.0931.5517.8
6.165099.710.0851.4997.6
ReflectionResolution: 2.3→50 Å / Num. all: 52679 / Num. obs: 52679 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.096 / Χ2: 0.928
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.343 / Num. unique all: 3480 / Χ2: 0.678 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.68 / Reflection: 39096 / Reflection acentric: 38008 / Reflection centric: 1088
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
2.5-2.70.290.280.3265176400117
2.7-3.10.480.480.511161411390224
3.1-3.60.730.730.7668476680167
3.6-4.50.840.840.8368566646210
4.5-7.10.810.820.7554665240226
7.1-29.8710.870.870.8117961652144

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.47 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 168545.406 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 5220 10.2 %RANDOM
Rwork0.216 ---
all0.219 52864 --
obs0.219 51331 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.117 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-8.54 Å20 Å25.05 Å2
2---2.02 Å20 Å2
3----6.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-10 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 100 446 8460
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 804 10.1 %
Rwork0.273 7120 -
obs-7924 90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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