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- PDB-2h4u: Crystal Structure of Human Thioesterase Superfamily Member 2 -

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Basic information

Entry
Database: PDB / ID: 2h4u
TitleCrystal Structure of Human Thioesterase Superfamily Member 2
ComponentsThioesterase superfamily member 2
KeywordsHYDROLASE / THIOESTERASE / Structural Genomics / Structural Genomics Consortium / SGC
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOgg, D.J. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Grasslund, S. / Flodin, S. / Hammerstrom, M. / Hogbom, M. ...Ogg, D.J. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Grasslund, S. / Flodin, S. / Hammerstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.-G. / Weigelt, J. / Hallberg, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human thioesterase superfamily member 2
Authors: Ogg, D.J. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Grasslund, S. / Flodin, S. / Hammerstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / ...Authors: Ogg, D.J. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Grasslund, S. / Flodin, S. / Hammerstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.-G. / Weigelt, J. / Hallberg, M.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)62,6404
Polymers62,6404
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-30 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.050, 90.970, 114.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 20 - 139 / Label seq-ID: 25 - 144

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Thioesterase superfamily member 2


Mass: 15659.983 Da / Num. of mol.: 4 / Fragment: residues 19-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) / References: UniProt: Q9NPJ3, acetyl-CoA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20 % PEG 3350, 0.2M Na/K phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2006 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 30948 / Num. obs: 30821 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.58
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 7.5 / Num. unique all: 6965 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1WN3

1wn3


Resolution: 2.2→19.55 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.062 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.259 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27189 1538 5 %RANDOM
Rwork0.21698 ---
obs0.21969 29216 99.55 %-
all-30894 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3662 0 0 211 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9745012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.8224.72125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14915686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9521516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022623
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.21753
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22494
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.30.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7421.52486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14123917
X-RAY DIFFRACTIONr_scbond_it1.77731307
X-RAY DIFFRACTIONr_scangle_it2.8674.51095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 886 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.425
2Bloose positional0.375
3Cloose positional0.435
4Dloose positional0.55
1Aloose thermal2.510
2Bloose thermal2.4510
3Cloose thermal3.110
4Dloose thermal2.5410
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 110 -
Rwork0.298 2100 -
obs--99.82 %

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