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- PDB-3fo5: Human START domain of Acyl-coenzyme A thioesterase 11 (ACOT11) -

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Basic information

Entry
Database: PDB / ID: 3fo5
TitleHuman START domain of Acyl-coenzyme A thioesterase 11 (ACOT11)
ComponentsThioesterase, adipose associated, isoform BFIT2
KeywordsLIPID TRANSPORT / Orthogonal Bundle / Consortium
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / long-chain fatty acyl-CoA binding / : / : / palmitoyl-CoA hydrolase / acyl-CoA metabolic process / fatty-acyl-CoA binding / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / Hydrolases; Acting on ester bonds; Thioester hydrolases ...long-chain fatty acyl-CoA hydrolase activity / long-chain fatty acyl-CoA binding / : / : / palmitoyl-CoA hydrolase / acyl-CoA metabolic process / fatty-acyl-CoA binding / fatty acyl-CoA hydrolase activity / Mitochondrial Fatty Acid Beta-Oxidation / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / negative regulation of cold-induced thermogenesis / response to temperature stimulus / response to cold / fatty acid metabolic process / intracellular signal transduction / mitochondrial matrix / lipid binding / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Thioesterase domain / Thioesterase superfamily / START domain ...Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / Thioesterase domain / Thioesterase superfamily / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / HotDog domain superfamily / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3,3',3''-phosphanetriyltripropanoic acid / Acyl-coenzyme A thioesterase 11 / Acyl-coenzyme A thioesterase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSiponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van-Den-Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Wisniewska, M. / Shueler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Comparative structural analysis of lipid binding START domains.
Authors: Thorsell, A.G. / Lee, W.H. / Persson, C. / Siponen, M.I. / Nilsson, M. / Busam, R.D. / Kotenyova, T. / Schuler, H. / Lehtio, L.
History
DepositionDec 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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, adipose associated, isoform BFIT2
B: Thioesterase, adipose associated, isoform BFIT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1917
Polymers59,3372
Non-polymers8545
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-29 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.440, 130.080, 165.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioesterase, adipose associated, isoform BFIT2 / Acyl-CoA thioesterase 11 / Acyl-CoA thioesterase 11 / isoform CRA_b


Mass: 29668.473 Da / Num. of mol.: 2 / Fragment: STARTdomain, UNP residues 339-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOT11, hCG_33028, RP11-240D10.1-002 / Plasmid: LEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52LP1, UniProt: Q8WXI4*PLUS

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid


Mass: 250.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15O6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3748.2
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop5.50.2M Magnesium chloride, 0.1M Bis-tris, pH5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop5.50.2M Ammonium formate, 20% PEG3350, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONBESSY 14.220.97985, 0.97973, 0.97201
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJun 26, 2008mirrors
RAYONIX MX225HE2CCDJun 26, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.979851
30.979731
40.972011
ReflectionResolution: 2→40 Å / Num. obs: 37936 / Observed criterion σ(F): 12.7 / Observed criterion σ(I): 15.34 / Redundancy: 6.4 % / Biso Wilson estimate: 14.023 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 15.34
Reflection shellResolution: 2→2.1 Å / Redundancy: 63.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.57 / Num. unique all: 5156 / Rsym value: 0.73

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0044refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.139 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.186 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25122 1897 5 %RANDOM
Rwork0.20222 ---
all0.20466 36038 --
obs0.20466 36038 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.1 Å2
Refine analyzeLuzzati coordinate error free: 0.171 Å
Refinement stepCycle: LAST / Resolution: 2→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 55 168 4033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223967
X-RAY DIFFRACTIONr_bond_other_d0.0010.022710
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9655376
X-RAY DIFFRACTIONr_angle_other_deg0.823.0016541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26223.594192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18615654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_mcbond_it0.7211.52366
X-RAY DIFFRACTIONr_mcbond_other0.181.5937
X-RAY DIFFRACTIONr_mcangle_it1.35823844
X-RAY DIFFRACTIONr_scbond_it2.13831601
X-RAY DIFFRACTIONr_scangle_it3.4734.51531
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 139 -
Rwork0.255 2644 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5754-0.8371.07242.1844-0.9241.5430.02480.13280.1690.1619-0.167-0.25660.03280.19890.14220.0283-0.00250.00440.13390.01380.088810.19845.5957.471
21.5971-0.0021-0.20782.97570.5391.4035-0.00970.0675-0.15590.4715-0.1082-0.12870.2630.05490.11790.19720.0306-0.04250.04040.01370.083415.89513.07671.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A346 - 584
2X-RAY DIFFRACTION2B352 - 592

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