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- PDB-1sg4: Crystal structure of human mitochondrial delta3-delta2-enoyl-CoA ... -

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Basic information

Entry
Database: PDB / ID: 1sg4
TitleCrystal structure of human mitochondrial delta3-delta2-enoyl-CoA isomerase
Components3,2-trans-enoyl-CoA isomerase, mitochondrial
KeywordsISOMERASE / crotonase fold
Function / homology
Function and homology information


mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
OCTANOYL-COENZYME A / Enoyl-CoA delta isomerase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsPartanen, S.T. / Novikov, D.K. / Popov, A.N. / Mursula, A.M. / Hiltunen, J.K. / Wierenga, R.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The 1.3 A crystal structure of human mitochondrial Delta3-Delta2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group.
Authors: Partanen, S.T. / Novikov, D.K. / Popov, A.N. / Mursula, A.M. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionFeb 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
B: 3,2-trans-enoyl-CoA isomerase, mitochondrial
C: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7484
Polymers85,8543
Non-polymers8941
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-35 kcal/mol
Surface area29390 Å2
MethodPISA
2
A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
B: 3,2-trans-enoyl-CoA isomerase, mitochondrial
C: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules

A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
B: 3,2-trans-enoyl-CoA isomerase, mitochondrial
C: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,4958
Polymers171,7086
Non-polymers1,7872
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15550 Å2
ΔGint-79 kcal/mol
Surface area56250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.984, 78.288, 113.209
Angle α, β, γ (deg.)90.00, 116.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3,2-trans-enoyl-CoA isomerase, mitochondrial / Dodecenoyl-CoA delta-isomerase


Mass: 28617.965 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCI / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P42126, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-CO8 / OCTANOYL-COENZYME A / Octanoyl-CoA


Mass: 893.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: PEG 6000, sodium acetate, sodium cloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1310.802
SYNCHROTRONEMBL/DESY, HAMBURG X1320.9202, 0.9184, 0.8500
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDMay 10, 2002bent mirrors
MARRESEARCH2CCDMay 10, 2002bent mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1triangularSINGLE WAVELENGTHMx-ray1
2triangularMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.8021
20.92021
30.91841
40.851
ReflectionResolution: 1.3→20 Å / Num. obs: 182696 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.3
Reflection shellResolution: 1.3→1.31 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5263 / % possible all: 82.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.202 9150 random
Rwork0.157 --
obs0.157 173546 -
all-182696 -
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 0 57 667 6800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_zero_chiral_vol0.064
LS refinement shell
Resolution (Å)Rfactor RworkRefine-ID
1.3-1.360.231X-RAY DIFFRACTION
1.36-1.410.213X-RAY DIFFRACTION

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