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- PDB-4gah: Human acyl-CoA thioesterases 4 in complex with undecan-2-one-CoA ... -

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Basic information

Entry
Database: PDB / ID: 4gah
TitleHuman acyl-CoA thioesterases 4 in complex with undecan-2-one-CoA inhibitor
ComponentsThioesterase superfamily member 4
Keywordshydrolase/hydrolase inhibitor / hotdog fold / acyl CoA hydrolase / akt c-terminal modulating protein / acyl-CoA / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


: / : / palmitoyl-CoA hydrolase / Negative regulation of the PI3K/AKT network / Activation of AKT2 / Mitochondrial Fatty Acid Beta-Oxidation / regulation of mitochondrial membrane permeability involved in apoptotic process / CD28 dependent PI3K/Akt signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / VEGFR2 mediated vascular permeability ...: / : / palmitoyl-CoA hydrolase / Negative regulation of the PI3K/AKT network / Activation of AKT2 / Mitochondrial Fatty Acid Beta-Oxidation / regulation of mitochondrial membrane permeability involved in apoptotic process / CD28 dependent PI3K/Akt signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / VEGFR2 mediated vascular permeability / fatty acid metabolic process / mitochondrial intermembrane space / ruffle membrane / PIP3 activates AKT signaling / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-0ET / Acyl-coenzyme A thioesterase THEM4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLim, K. / Pathak, M.C. / Herzberg, O.
Citation
Journal: Biochemistry / Year: 2012
Title: Correlation of structure and function in the human hotdog-fold enzyme hTHEM4.
Authors: Zhao, H. / Lim, K. / Choudry, A. / Latham, J.A. / Pathak, M.C. / Dominguez, D. / Luo, L. / Herzberg, O. / Dunaway-Mariano, D.
#1: Journal: Biochemistry / Year: 2009
Title: The Akt C-Terminal modulator protein is an acyl-CoA thioesterase of the hotdog-fold family
Authors: Zhao, H. / Martin, B. / Bisoffi, M. / Dunaway-Mariano, D.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Thioesterase superfamily member 4
B: Thioesterase superfamily member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7395
Polymers47,9262
Non-polymers2,8133
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-21 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.608, 58.777, 135.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioesterase superfamily member 4 / Carboxyl-terminal modulator protein


Mass: 23962.758 Da / Num. of mol.: 2 / Fragment: residues 40-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTMP, THEM4 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21codon plus(DE3) RIL / References: UniProt: Q5T1C6, acyl-CoA hydrolase
#2: Chemical ChemComp-0ET / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-[(2R)-2-oxidanylundecyl]sulfanylethylamino]propyl]amino]butyl] hydrogen phosphate / undecan-2-one-CoA


Mass: 937.826 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H58N7O17P3S
#3: 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 1:1 protein and reservoir solution. Reservoir: 11 % w/v PEG 3350 and 0.1 M ammonium phosphate monobasic. Proteins: 8 mg/mL in kept in 0.2 M NaCl and 50 mM HEPES (pH 7.5), 4 mM undecan-2-one- ...Details: 1:1 protein and reservoir solution. Reservoir: 11 % w/v PEG 3350 and 0.1 M ammonium phosphate monobasic. Proteins: 8 mg/mL in kept in 0.2 M NaCl and 50 mM HEPES (pH 7.5), 4 mM undecan-2-one-CoA., VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9202 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.3→43.5 Å / Num. all: 20650 / Num. obs: 20650 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2033 / % possible all: 99.9

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OV9

2ov9


Resolution: 2.3→43.5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 1001 random
Rwork0.19 --
all-20650 -
obs-20649 -
Refinement stepCycle: LAST / Resolution: 2.3→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 136 211 3250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.4
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.323 93 -
Rwork0.251 --
obs-2033 99.9 %

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