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- PDB-3f5o: Crystal Structure of hTHEM2(undecan-2-one-CoA) complex -

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Basic information

Entry
Database: PDB / ID: 3f5o
TitleCrystal Structure of hTHEM2(undecan-2-one-CoA) complex
ComponentsThioesterase superfamily member 2
KeywordsHYDROLASE / hotdog 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
COENZYME A / undecan-2-one / Acyl-coenzyme A thioesterase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXu, H. / Gong, W.
CitationJournal: Biochemistry / Year: 2009
Title: The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis
Authors: Cao, J. / Xu, H. / Zhao, H. / Gong, W. / Dunaway-Mariano, D.
History
DepositionNov 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)137,30135
Polymers128,4218
Non-polymers8,88027
Water15,313850
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)68,63317
Polymers64,2114
Non-polymers4,42213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-66 kcal/mol
Surface area19020 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)68,66818
Polymers64,2114
Non-polymers4,45814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-80 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.032, 110.632, 119.819
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Thioesterase superfamily member 2


Mass: 16052.646 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPJ3

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Non-polymers , 5 types, 877 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-UOC / undecan-2-one


Mass: 170.292 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H22O
#4: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.1M ammonium citrate, dibasic, 5-10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 134034 / % possible obs: 99.1 %
Reflection shellResolution: 1.7→1.76 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F0X

2f0x


Resolution: 1.7→20.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23701 6645 5 %RANDOM
Rwork0.19861 ---
obs0.20051 125902 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.255 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2--1.17 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8223 0 527 850 9600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228861
X-RAY DIFFRACTIONr_angle_refined_deg1.8212.03312006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5951140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31724.491265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.988151582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1791539
X-RAY DIFFRACTIONr_chiral_restr0.6510.21503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026005
X-RAY DIFFRACTIONr_nbd_refined0.2180.24467
X-RAY DIFFRACTIONr_nbtor_refined0.2960.26089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2813
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.220
X-RAY DIFFRACTIONr_mcbond_it0.851.55491
X-RAY DIFFRACTIONr_mcangle_it1.44428888
X-RAY DIFFRACTIONr_scbond_it2.11833370
X-RAY DIFFRACTIONr_scangle_it3.174.53093
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 458 -
Rwork0.318 9054 -
obs--97.35 %

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