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- PDB-4zv3: Crystal structure of the N- and C-terminal domains of mouse acyl-... -

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Basic information

Entry
Database: PDB / ID: 4zv3
TitleCrystal structure of the N- and C-terminal domains of mouse acyl-CoA thioesterase 7
ComponentsCytosolic acyl coenzyme A thioester hydrolase
KeywordsHYDROLASE / Thioesterase / Double hotdog / Inflammation
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / palmitic acid biosynthetic process / 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 ...long-chain fatty acyl-CoA hydrolase activity / palmitic acid biosynthetic process / 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 / extracellular exosome / nucleoplasm / identical protein binding / 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 / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Cytosolic acyl coenzyme A thioester hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSwarbrick, C.M.D. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal structure of the N- and C-terminal domains of mouse acyl-CoA thioesterase 7
Authors: Swarbrick, C.M.D. / Forwood, J.K.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic acyl coenzyme A thioester hydrolase
B: Cytosolic acyl coenzyme A thioester hydrolase
C: Cytosolic acyl coenzyme A thioester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5556
Polymers106,2533
Non-polymers2,3033
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-38 kcal/mol
Surface area38800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.847, 106.924, 79.864
Angle α, β, γ (deg.)90.00, 112.32, 90.00
Int Tables number4
Space group name H-MP1211

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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: 35417.508 Da / Num. of mol.: 3 / Fragment: unp residues 55-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acot7, Bach / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLySs / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium citrate, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→34.91 Å / Num. obs: 18941 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 5.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2B, 2V1O

2q2b

2v1o


Resolution: 3.1→32.1 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.872 / SU B: 0.015 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.589 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29609 967 5.1 %RANDOM
Rwork0.24108 ---
obs0.24408 17973 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.1→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 144 0 7131
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 56 -
Rwork0.346 1356 -
obs--100 %

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