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- PDB-4u19: Crystal structure of human peroxisomal delta3,delta2, enoyl-CoA i... -

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Basic information

Entry
Database: PDB / ID: 4u19
TitleCrystal structure of human peroxisomal delta3,delta2, enoyl-CoA isomerase V349A mutant (ISOA-ECI2)
ComponentsEnoyl-CoA delta isomerase 2
KeywordsISOMERASE / PECI / enoy-CoA isomerase / crotonase / beta-oxidation
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle ...Beta-oxidation of very long chain fatty acids / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / 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 ...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 / FERM/acyl-CoA-binding protein superfamily / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 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: 1.88 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 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Enoyl-CoA delta isomerase 2
C: Enoyl-CoA delta isomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7797
Polymers91,6113
Non-polymers1684
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-70 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.609, 123.690, 128.933
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
11B
21A
12C
22A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 103 - 348 / Label seq-ID: 24 - 269

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.791678, 0.587994, -0.165861), (0.4115, -0.312545, 0.856145), (0.451568, -0.746042, -0.489394)13.48148, -44.72408, 34.43019
3given(1), (1), (1)
4given(0.786688, 0.414148, 0.457825), (0.591566, -0.293617, -0.750892), (-0.176555, 0.861551, -0.475981)-7.99126, 4.30782, 57.06277

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Components

#1: Protein Enoyl-CoA delta isomerase 2 / 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: 30536.844 Da / Num. of mol.: 3 / Fragment: UNP residues 138-390 / Mutation: yes
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: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 10% PEG 6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / 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: 1.88→47.61 Å / Num. obs: 62659 / % possible obs: 99.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 12
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 7 % / Rmerge(I) obs: 1.441 / Mean I/σ(I) obs: 1.5 / % possible all: 96.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F6Q

2f6q


Resolution: 1.88→47.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.046 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23441 3172 5.1 %RANDOM
Rwork0.18387 ---
obs0.18645 59362 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å20 Å2-0 Å2
2---2.19 Å20 Å2
3----2.22 Å2
Refinement stepCycle: 1 / Resolution: 1.88→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 7 273 6049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195916
X-RAY DIFFRACTIONr_bond_other_d0.0010.025717
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9648003
X-RAY DIFFRACTIONr_angle_other_deg0.875313203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92624.36250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.945151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3631532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
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_it2.9363.5482991
X-RAY DIFFRACTIONr_mcbond_other2.9343.5472990
X-RAY DIFFRACTIONr_mcangle_it4.0665.2893732
X-RAY DIFFRACTIONr_mcangle_other4.0665.2913733
X-RAY DIFFRACTIONr_scbond_it4.014.0512925
X-RAY DIFFRACTIONr_scbond_other4.014.0512925
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0735.8794268
X-RAY DIFFRACTIONr_long_range_B_refined7.68429.0176844
X-RAY DIFFRACTIONr_long_range_B_other7.68329.026845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B3654loose positional0.435
22C3673loose positional0.475
11B3654loose thermal5.4210
22C3673loose thermal4.5610
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 221 -
Rwork0.374 4105 -
obs--94.64 %

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