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- PDB-6vfy: Crystal structure of mouse acyl-CoA thioesterase 7 with CoA -

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Basic information

Entry
Database: PDB / ID: 6vfy
TitleCrystal structure of mouse acyl-CoA thioesterase 7 with CoA
ComponentsCytosolic acyl coenzyme A thioester hydrolase
KeywordsHYDROLASE / Thioesterase / Coenzyme A
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / Mitochondrial Fatty Acid Beta-Oxidation / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid catabolic process / carboxylic ester hydrolase activity / mitochondrial matrix / neuron projection / neuronal cell body ...long-chain fatty acyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / Mitochondrial Fatty Acid Beta-Oxidation / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid catabolic process / carboxylic ester hydrolase activity / mitochondrial matrix / neuron projection / neuronal cell body / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / PHOSPHATE ION / Cytosolic acyl coenzyme A thioester hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsTeakel, S.L. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal structure of mouse acyl-CoA thioesterase 7 with CoA
Authors: Teakel, S.L. / Forwood, J.K.
History
DepositionJan 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Cytosolic acyl coenzyme A thioester hydrolase
E: Cytosolic acyl coenzyme A thioester hydrolase
F: Cytosolic acyl coenzyme A thioester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4387
Polymers113,0403
Non-polymers2,3984
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-42 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.156, 135.331, 70.126
Angle α, β, γ (deg.)90.000, 100.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain D and ((resid 58 and (name N or name...
21(chain E and ((resid 58 and (name N or name...
31(chain F and (resid 58 through 66 or (resid 67...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILE(chain D and ((resid 58 and (name N or name...DA5824
12ILEILECOACOA(chain D and ((resid 58 and (name N or name...DA - D58 - 40124
13ILEILECOACOA(chain D and ((resid 58 and (name N or name...DA - D58 - 40124
14ILEILECOACOA(chain D and ((resid 58 and (name N or name...DA - D58 - 40124
15ILEILECOACOA(chain D and ((resid 58 and (name N or name...DA - D58 - 40124
21ILEILEILEILE(chain E and ((resid 58 and (name N or name...EB5824
22ILEILECOACOA(chain E and ((resid 58 and (name N or name...EB - E58 - 40124
23ILEILECOACOA(chain E and ((resid 58 and (name N or name...EB - E58 - 40124
24ILEILECOACOA(chain E and ((resid 58 and (name N or name...EB - E58 - 40124
25ILEILECOACOA(chain E and ((resid 58 and (name N or name...EB - E58 - 40124
31ILEILEPROPRO(chain F and (resid 58 through 66 or (resid 67...FC58 - 6624 - 32
32ASPASPASPASP(chain F and (resid 58 through 66 or (resid 67...FC6733
33ILEILECOACOA(chain F and (resid 58 through 66 or (resid 67...FC - F58 - 40124
34ILEILECOACOA(chain F and (resid 58 through 66 or (resid 67...FC - F58 - 40124
35ILEILECOACOA(chain F and (resid 58 through 66 or (resid 67...FC - F58 - 40124
36ILEILECOACOA(chain F and (resid 58 through 66 or (resid 67...FC - F58 - 40124

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Components

#1: Protein Cytosolic acyl coenzyme A thioester hydrolase / Acyl-CoA thioesterase 7 / Brain acyl-CoA hydrolase / BACH / CTE-IIa / CTE-II / Long chain acyl-CoA ...Acyl-CoA thioesterase 7 / Brain acyl-CoA hydrolase / BACH / CTE-IIa / CTE-II / Long chain acyl-CoA thioester hydrolase


Mass: 37680.117 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acot7, Bach / Production host: Escherichia coli (E. coli) / References: UniProt: Q91V12, palmitoyl-CoA hydrolase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / Details: 0.1M Ammonium citrate pH 7, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.6→29.77 Å / Num. obs: 37634 / % possible obs: 99.5 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.033 / Rrim(I) all: 0.09 / Net I/σ(I): 11.4 / Num. measured all: 269468 / Scaling rejects: 419
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.727.41.5213359245550.7150.5981.6361.399
9.01-29.777.10.04864769150.9980.0190.05230.697.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZV3

4zv3


Resolution: 2.6→29.77 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.97
RfactorNum. reflection% reflection
Rfree0.2676 1939 5.16 %
Rwork0.2308 --
obs0.2327 37571 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.59 Å2 / Biso mean: 87.3461 Å2 / Biso min: 39.59 Å2
Refinement stepCycle: final / Resolution: 2.6→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 149 3 6718
Biso mean--82.09 64.88 -
Num. residues----910
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D2820X-RAY DIFFRACTION9.269TORSIONAL
12E2820X-RAY DIFFRACTION9.269TORSIONAL
13F2820X-RAY DIFFRACTION9.269TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6001-2.66510.44981270.3728251199
2.6651-2.73710.3261280.3373253799
2.7371-2.81760.35151300.324255699
2.8176-2.90850.40211350.3239252299
2.9085-3.01230.36721380.3119251899
3.0123-3.13280.34931440.2862252899
3.1328-3.27520.35761460.2854251599
3.2752-3.44770.31021440.27492541100
3.4477-3.66330.33951470.2636256499
3.6633-3.94560.30831400.24512534100
3.9456-4.34150.23431610.2072529100
4.3415-4.96720.21861470.17712561100
4.9672-6.24870.23471240.21342600100
6.2487-29.770.20011280.19562616100

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