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- PDB-4xjv: Crystal structure of human thioesterase 2 -

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Basic information

Entry
Database: PDB / ID: 4xjv
TitleCrystal structure of human thioesterase 2
ComponentsS-acyl fatty acid synthase thioesterase, medium chain
KeywordsHYDROLASE / closed conformation / fatty acid synthase / lipid metabolism
Function / homology
Function and homology information


: / medium-chain fatty acid biosynthetic process / : / : / : / Fatty acyl-CoA biosynthesis / oleoyl-[acyl-carrier-protein] hydrolase / lipid biosynthetic process / cytosol
Similarity search - Function
Thioesterase type II, NRPS/PKS/S-FAS / Thioesterase / Thioesterase domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-acyl fatty acid synthase thioesterase, medium chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRitchie, M.K. / Kridel, S.J. / Lowther, W.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA411401 United States
Department of Defense, PCRPPC08165 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure and Substrate Specificity of Human Thioesterase 2: INSIGHTS INTO THE MOLECULAR BASIS FOR THE MODULATION OF FATTY ACID SYNTHASE.
Authors: Ritchie, M.K. / Johnson, L.C. / Clodfelter, J.E. / Pemble, C.W. / Fulp, B.E. / Furdui, C.M. / Kridel, S.J. / Lowther, W.T.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-acyl fatty acid synthase thioesterase, medium chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6352
Polymers30,6001
Non-polymers351
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.070, 96.070, 159.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein S-acyl fatty acid synthase thioesterase, medium chain / Augmented in rheumatoid arthritis 1 / AURA1 / Oleoyl-ACP hydrolase / Thioesterase II / Thioesterase ...Augmented in rheumatoid arthritis 1 / AURA1 / Oleoyl-ACP hydrolase / Thioesterase II / Thioesterase domain-containing protein 1


Mass: 30599.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLAH, THEDC1 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: Q9NV23, oleoyl-[acyl-carrier-protein] hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.02 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Rod-shaped crystals of TE2 (10 mg/ml with 10 mM fresh DTT) were grown using the vapor diffusion method at 25 C, using a 1:1 drop to well ratio. The well solutions contained 1.64 M NaH2PO4, 0. ...Details: Rod-shaped crystals of TE2 (10 mg/ml with 10 mM fresh DTT) were grown using the vapor diffusion method at 25 C, using a 1:1 drop to well ratio. The well solutions contained 1.64 M NaH2PO4, 0.42 M K2HPO4 and 50 mM HEPES. Crystals were cryoprotected by transfer to paratone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→24.817 Å / Num. all: 9601 / Num. obs: 9601 / % possible obs: 99.9 % / Redundancy: 11.7 % / Biso Wilson estimate: 66.47 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.98 / Net I/σ(I): 12.8 / Num. measured all: 113166 / Scaling rejects: 849
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.8-2.911.820.4872.9113809501.44153100
2.9-3.0211.830.383.7111909381.3194100
3.02-3.1511.910.3154.6111189281.1767100
3.15-3.3211.90.2645.1113549461.1896100
3.32-3.5311.890.1956.4113469451.07106100
3.53-3.811.860.1479.9112119420.7938100
3.8-4.1811.870.09613.8115429660.8575100
4.18-4.7911.730.07519113649650.742100
4.79-6.0311.480.05822.8112429760.6837100
6.03-67.9310.790.03139.11141910450.6614199.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
d*TREK9.9.9.1Ldata reduction
PDB_EXTRACT3.15data extraction
d*TREK9.9.9.1Ldata scaling
PHENIX1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FLB
Resolution: 2.8→24.817 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3449 473 5.06 %
Rwork0.2944 8880 -
obs0.2969 9353 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.62 Å2 / Biso mean: 94.6564 Å2 / Biso min: 50.72 Å2
Refinement stepCycle: final / Resolution: 2.8→24.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 1 0 1703
Biso mean--79.12 --
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031745
X-RAY DIFFRACTIONf_angle_d0.7252363
X-RAY DIFFRACTIONf_chiral_restr0.028261
X-RAY DIFFRACTIONf_plane_restr0.003301
X-RAY DIFFRACTIONf_dihedral_angle_d13.216628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8002-3.20460.411530.37392925307898
3.2046-4.03470.42771550.32792849300495
4.0347-24.81820.29741650.26133106327199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.54323.7442-2.81684.1092-4.75517.5914-0.0979-1.42060.16090.18850.3378-1.4241-0.53982.096-0.24610.80330.3475-0.0891.1736-0.39861.06837.031-30.305-22.3035
24.7702-0.2833-0.02725.74492.35226.2069-0.2017-1.03241.2996-0.62061.7752-1.0838-0.04931.6565-1.44371.30780.11480.14720.7777-0.32531.04981.9031-20.1528-28.5382
35.3503-2.0166-5.29283.51413.95796.6016-0.1201-0.19730.16030.05620.33390.191-0.21890.0501-0.24880.6940.3525-0.03330.6396-0.05330.6597-11.1142-26.492-19.3782
44.86814.40845.29094.38364.93465.79870.7453-2.3702-0.41830.7583-1.6954-0.50881.2392-1.04630.96071.290.263-0.17471.47470.24920.5421-4.3599-27.37322.772
52.55051.91551.90119.01544.76892.8999-0.5053-0.39650.6869-0.9161-0.47210.7631-1.4895-1.61730.96340.70880.27910.05880.7733-0.14540.7403-11.9613-20.9849-14.927
68.0474-3.5289-1.02376.28440.95485.1125-0.3833-0.615-0.11850.42720.46480.21260.2396-0.0274-0.0950.75280.3051-0.00560.6561-0.06110.5452-4.105-39.4683-24.9266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 25:51)A25 - 51
2X-RAY DIFFRACTION2(chain A and resid 52:95)A52 - 95
3X-RAY DIFFRACTION3(chain A and resid 96:156)A96 - 156
4X-RAY DIFFRACTION4(chain A and resid 157:173)A157 - 173
5X-RAY DIFFRACTION5(chain A and resid 174:199)A174 - 199
6X-RAY DIFFRACTION6(chain A and resid 200:265)A200 - 265

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