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- PDB-4u18: Crystal structure of human peroxisomal delta3,delta2, enoyl-CoA i... -

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Basic information

Entry
Database: PDB / ID: 4u18
TitleCrystal structure of human peroxisomal delta3,delta2, enoyl-CoA isomerase (ISO-ECI2)
ComponentsEnoyl-CoA delta isomerase 2, mitochondrial
KeywordsISOMERASE / PECI / enoy-CoA isomerase / crotonase / beta-oxidation
Function / homology
Function and homology information


Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle ...Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle / mitochondrion / membrane / cytosol
Similarity search - Function
Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase ...Acyl-CoA-binding protein, ACBP, conserved site / Acyl-CoA-binding (ACB) domain signature. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / FERM/acyl-CoA-binding protein superfamily / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA delta isomerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsOnwukwe, G.U. / Koski, M.K. / Wierenga, R.K.
Funding support Germany, 1items
OrganizationGrant numberCountry
Biostruct-XN283570 Germany
CitationJournal: Febs J. / Year: 2015
Title: Human Delta (3) , Delta (2) -enoyl-CoA isomerase, type 2: a structural enzymology study on the catalytic role of its ACBP domain and helix-10.
Authors: Onwukwe, G.U. / Kursula, P. / Koski, M.K. / Schmitz, W. / Wierenga, R.K.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA delta isomerase 2, mitochondrial
B: Enoyl-CoA delta isomerase 2, mitochondrial
C: Enoyl-CoA delta isomerase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8937
Polymers91,6953
Non-polymers1984
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-75 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.428, 91.915, 130.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 3

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA105 - 34726 - 268
21ASNASNBB105 - 34726 - 268
12VALVALAA105 - 34926 - 270
22VALVALCC105 - 34926 - 270

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.46548, 0.141397, 0.873691), (0.319532, 0.947425, 0.016908), (-0.825365, 0.287042, -0.486188)40.64006, -7.03859, 4.88424
3given(1), (1), (1)
4given(-0.46967, 0.333747, -0.817327), (0.110046, 0.940702, 0.320889), (0.875956, 0.060768, -0.478547)23.76754, 0.86201, -37.38311

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Components

#1: Protein Enoyl-CoA delta isomerase 2, mitochondrial / DRS-1 / Delta(3) / delta(2)-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / Diazepam-binding ...DRS-1 / Delta(3) / delta(2)-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / Diazepam-binding inhibitor-related protein 1 / DBI-related protein 1 / Dodecenoyl-CoA isomerase / Hepatocellular carcinoma-associated antigen 88 / Peroxisomal 3 / 2-trans-enoyl-CoA isomerase / pECI / Renal carcinoma antigen NY-REN-1


Mass: 30564.895 Da / Num. of mol.: 3 / Fragment: UNP residues 138-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECI2, DRS1, HCA88, PECI / Production host: Escherichia coli (E. coli)
References: UniProt: O75521, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES pH 6.5, 1M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.64→49.6 Å / Num. obs: 27223 / % possible obs: 98.4 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.5
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.222 / Mean I/σ(I) obs: 1.4 / % possible all: 87.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→75.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.873 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.768 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1365 5 %RANDOM
Rwork0.19432 ---
obs0.19764 25794 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å2-0 Å2
2--9.93 Å2-0 Å2
3----7.59 Å2
Refinement stepCycle: 1 / Resolution: 2.64→75.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 9 21 5773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195863
X-RAY DIFFRACTIONr_bond_other_d0.0020.025672
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9657932
X-RAY DIFFRACTIONr_angle_other_deg0.883313093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13124.472246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.856151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1431530
X-RAY DIFFRACTIONr_chiral_restr0.0750.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216573
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1357.5712964
X-RAY DIFFRACTIONr_mcbond_other6.127.572963
X-RAY DIFFRACTIONr_mcangle_it8.88511.353698
X-RAY DIFFRACTIONr_mcangle_other8.88711.3523699
X-RAY DIFFRACTIONr_scbond_it7.4348.3252899
X-RAY DIFFRACTIONr_scbond_other7.4348.3252899
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.22412.1924235
X-RAY DIFFRACTIONr_long_range_B_refined13.85461.196622
X-RAY DIFFRACTIONr_long_range_B_other13.85461.196622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
112230loose positional0.045
222316loose positional0.045
111379tight thermal14.950.5
221441tight thermal8.530.5
112230loose thermal14.4910
222316loose thermal9.4910
LS refinement shellResolution: 2.642→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.547 89 -
Rwork0.444 1590 -
obs--83.41 %

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