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- PDB-4ae8: Crystal structure of human THEM4 -

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Basic information

Entry
Database: PDB / ID: 4ae8
TitleCrystal structure of human THEM4
ComponentsTHIOESTERASE SUPERFAMILY MEMBER 4
KeywordsHYDROLASE / HOTDOG-FOLD
Function / homology
Function and homology information


palmitoyl-CoA hydrolase / long-chain fatty acyl-CoA hydrolase activity / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / VEGFR2 mediated vascular permeability / fatty acid metabolic process ...palmitoyl-CoA hydrolase / long-chain fatty acyl-CoA hydrolase activity / 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 / negative regulation of 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
Acyl-coenzyme A thioesterase THEM4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.594 Å
AuthorsZhuravleva, E. / Gut, H. / Hynx, D. / Marcellin, D. / Bleck, C.K.E. / Genoud, C. / Cron, P. / Keusch, J.J. / Dummler, B. / Degli Esposti, M. / Hemmings, B.A.
CitationJournal: Mol.Cell.Biol. / Year: 2012
Title: Acyl Coenzyme a Thioesterase Them5/Acot15 is Involved in Cardiolipin Remodeling and Fatty Liver Development.
Authors: Zhuravleva, E. / Gut, H. / Hynx, D. / Marcellin, D. / Bleck, C.K.E. / Genoud, C. / Cron, P. / Keusch, J.J. / Dummler, B. / Esposti, M.D. / Hemmings, B.A.
History
DepositionJan 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOESTERASE SUPERFAMILY MEMBER 4
B: THIOESTERASE SUPERFAMILY MEMBER 4
C: THIOESTERASE SUPERFAMILY MEMBER 4
D: THIOESTERASE SUPERFAMILY MEMBER 4


Theoretical massNumber of molelcules
Total (without water)95,5754
Polymers95,5754
Non-polymers00
Water13,529751
1
A: THIOESTERASE SUPERFAMILY MEMBER 4
B: THIOESTERASE SUPERFAMILY MEMBER 4


Theoretical massNumber of molelcules
Total (without water)47,7872
Polymers47,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-16.9 kcal/mol
Surface area14830 Å2
MethodPISA
2
C: THIOESTERASE SUPERFAMILY MEMBER 4
D: THIOESTERASE SUPERFAMILY MEMBER 4


Theoretical massNumber of molelcules
Total (without water)47,7872
Polymers47,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-15.4 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.539, 58.211, 69.681
Angle α, β, γ (deg.)89.96, 71.14, 64.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.181, -0.9383, 0.2945), (-0.9356, 0.07206, -0.3456), (0.3031, -0.3381, -0.891)5.009, 6.258, 5.966
2given(-0.6138, -0.7342, -0.2902), (0.6426, -0.6782, 0.3566), (-0.4586, 0.03233, 0.888)62.4, -58.26, -8.178
3given(-0.6335, 0.7737, 0.005155), (0.7737, 0.6335, -0.002555), (-0.005242, 0.00237, -1)45.27, -53.63, 52.11

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Components

#1: Protein
THIOESTERASE SUPERFAMILY MEMBER 4 / CARBOXYL-TERMINAL MODULATOR PROTEIN


Mass: 23893.674 Da / Num. of mol.: 4 / Fragment: RESIDUES 37-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 / References: UniProt: Q5T1C6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 1.9 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growDetails: 30% PEG3000, 0.2M NACL, 0.1M TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.96
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 83501 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 14.97 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.2 / % possible all: 84

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.594→29.72 Å / SU ML: 0.43 / σ(F): 1.98 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 4113 4.9 %
Rwork0.1848 --
obs0.1867 83488 93.39 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.575 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.7986 Å2-3.2491 Å2-3.2969 Å2
2---0.8757 Å2-0.2947 Å2
3----0.9229 Å2
Refinement stepCycle: LAST / Resolution: 1.594→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5241 0 0 751 5992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065452
X-RAY DIFFRACTIONf_angle_d1.0237355
X-RAY DIFFRACTIONf_dihedral_angle_d12.2532045
X-RAY DIFFRACTIONf_chiral_restr0.073792
X-RAY DIFFRACTIONf_plane_restr0.005947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5941-1.61280.295940.25241971X-RAY DIFFRACTION67
1.6128-1.63250.2891330.23572461X-RAY DIFFRACTION84
1.6325-1.65310.30321400.24672548X-RAY DIFFRACTION88
1.6531-1.67490.26521410.22642683X-RAY DIFFRACTION91
1.6749-1.69780.24081170.22182664X-RAY DIFFRACTION91
1.6978-1.72210.28771310.21852750X-RAY DIFFRACTION93
1.7221-1.74780.26011530.21732763X-RAY DIFFRACTION94
1.7478-1.77510.3041410.20952746X-RAY DIFFRACTION94
1.7751-1.80420.25341560.20752748X-RAY DIFFRACTION94
1.8042-1.83530.26081500.20662797X-RAY DIFFRACTION95
1.8353-1.86870.25261390.19852764X-RAY DIFFRACTION95
1.8687-1.90460.23331510.19822769X-RAY DIFFRACTION95
1.9046-1.94350.24961580.19252833X-RAY DIFFRACTION94
1.9435-1.98570.23061400.19782742X-RAY DIFFRACTION95
1.9857-2.03190.24081240.19182804X-RAY DIFFRACTION95
2.0319-2.08270.23941510.19532797X-RAY DIFFRACTION95
2.0827-2.1390.21721430.19132794X-RAY DIFFRACTION95
2.139-2.20190.25761500.18482780X-RAY DIFFRACTION95
2.2019-2.2730.22311460.18362774X-RAY DIFFRACTION95
2.273-2.35420.24141580.17932747X-RAY DIFFRACTION95
2.3542-2.44840.20671260.18672815X-RAY DIFFRACTION95
2.4484-2.55980.2421420.19212816X-RAY DIFFRACTION96
2.5598-2.69470.22051380.17772836X-RAY DIFFRACTION96
2.6947-2.86340.22661540.18092786X-RAY DIFFRACTION96
2.8634-3.08420.21971250.18582840X-RAY DIFFRACTION96
3.0842-3.39420.19651640.16962833X-RAY DIFFRACTION97
3.3942-3.88440.19341400.15592866X-RAY DIFFRACTION97
3.8844-4.89040.16291590.14562806X-RAY DIFFRACTION97
4.8904-29.7250.22261490.20462842X-RAY DIFFRACTION97
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)
10.93560.5324-0.05910.8879-0.02350.19990.0316-0.0538-0.05270.0212-0.0261-0.11610.01820.0147-0.00730.06240.01980.00610.07560.00240.06721.3571-18.59419.8354
20.38170.18950.04191.30620.08620.25690.0056-0.0190.0449-0.0808-0.01790.12590.013-0.04090.00480.0854-0.0043-0.00420.0927-0.0040.061142.39853.736241.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR B
2X-RAY DIFFRACTION2CHAIN C OR D

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