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- PDB-4ae7: Crystal structure of human THEM5 -

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Basic information

Entry
Database: PDB / ID: 4ae7
TitleCrystal structure of human THEM5
ComponentsTHIOESTERASE SUPERFAMILY MEMBER 5
KeywordsHYDROLASE / HOTDOG-FOLD
Function / homology
Function and homology information


cardiolipin acyl-chain remodeling / long-chain fatty-acyl-CoA metabolic process / : / : / palmitoyl-CoA hydrolase / acyl-CoA metabolic process / Mitochondrial Fatty Acid Beta-Oxidation / fatty acid metabolic process / mitochondrial matrix
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 THEM5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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

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Assembly

Deposited unit
A: THIOESTERASE SUPERFAMILY MEMBER 5


Theoretical massNumber of molelcules
Total (without water)24,5361
Polymers24,5361
Non-polymers00
Water3,153175
1
A: THIOESTERASE SUPERFAMILY MEMBER 5

A: THIOESTERASE SUPERFAMILY MEMBER 5


Theoretical massNumber of molelcules
Total (without water)49,0722
Polymers49,0722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3530 Å2
ΔGint-25.8 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.389, 88.634, 105.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein THIOESTERASE SUPERFAMILY MEMBER 5


Mass: 24535.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-247
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: Q8N1Q8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsL206V, CORRESPONDS TO VAR_031766, DBSNP RS6587624

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 10% PEG 3000, 0.2 M NACL, 0.1 M PHOSPHATE-CITRATE PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 70847 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 16.07 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.1
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→27.519 Å / SU ML: 0.3 / σ(F): 1.25 / Phase error: 14.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1706 3503 5 %
Rwork0.1403 --
obs0.1418 70483 96.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.437 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.2185 Å20 Å20 Å2
2---2.8584 Å20 Å2
3----0.3601 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 0 175 1653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051534
X-RAY DIFFRACTIONf_angle_d1.0232072
X-RAY DIFFRACTIONf_dihedral_angle_d12.762574
X-RAY DIFFRACTIONf_chiral_restr0.07224
X-RAY DIFFRACTIONf_plane_restr0.005268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46990.26691260.23692684X-RAY DIFFRACTION97
1.4699-1.49090.22151580.2142636X-RAY DIFFRACTION97
1.4909-1.51310.25281310.20552763X-RAY DIFFRACTION97
1.5131-1.53680.21271370.18442574X-RAY DIFFRACTION96
1.5368-1.56190.1961450.17022771X-RAY DIFFRACTION97
1.5619-1.58890.1631510.1582637X-RAY DIFFRACTION97
1.5889-1.61780.18741420.13872708X-RAY DIFFRACTION98
1.6178-1.64890.16321570.1362674X-RAY DIFFRACTION98
1.6489-1.68250.14611330.13042716X-RAY DIFFRACTION98
1.6825-1.71910.15771370.1292706X-RAY DIFFRACTION98
1.7191-1.75910.15351040.1182742X-RAY DIFFRACTION98
1.7591-1.80310.16481520.11222694X-RAY DIFFRACTION98
1.8031-1.85180.16781420.10932760X-RAY DIFFRACTION98
1.8518-1.90630.13471460.10382715X-RAY DIFFRACTION98
1.9063-1.96780.1641450.11212710X-RAY DIFFRACTION98
1.9678-2.03810.16031450.10682711X-RAY DIFFRACTION99
2.0381-2.11970.15521450.11422716X-RAY DIFFRACTION99
2.1197-2.21610.13421400.1142742X-RAY DIFFRACTION99
2.2161-2.33290.17311450.11622719X-RAY DIFFRACTION98
2.3329-2.4790.18271410.13282734X-RAY DIFFRACTION98
2.479-2.67020.16181370.14242685X-RAY DIFFRACTION98
2.6702-2.93870.19661430.14532704X-RAY DIFFRACTION97
2.9387-3.36330.17391450.14092660X-RAY DIFFRACTION96
3.3633-4.23490.15111370.14012556X-RAY DIFFRACTION92
4.2349-27.52390.18931190.18642263X-RAY DIFFRACTION82

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