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- PDB-4zdb: Yeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA -

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Basic information

Entry
Database: PDB / ID: 4zdb
TitleYeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA
Components3,2-trans-enoyl-CoA isomerase
KeywordsISOMERASE / Crotonase / acetoacetyl-CoA / 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 / Peroxisomal protein import / fatty acid beta-oxidation / peroxisomal matrix / peroxisome
Similarity search - Function
: / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / 3,2-trans-enoyl-CoA isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsOnwukwe, G.U. / Koski, M.K. / Wierenga, R.K.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland141487 Finland
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of yeast peroxisomal Delta (3), Delta (2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the ...Title: Structures of yeast peroxisomal Delta (3), Delta (2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole.
Authors: Onwukwe, G.U. / Koski, M.K. / Pihko, P. / Schmitz, W. / Wierenga, R.K.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)105,86621
Polymers101,8983
Non-polymers3,96818
Water7,404411
1
A: 3,2-trans-enoyl-CoA isomerase
B: 3,2-trans-enoyl-CoA isomerase
C: 3,2-trans-enoyl-CoA isomerase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)211,73142
Polymers203,7956
Non-polymers7,93636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+5/21
Buried area33950 Å2
ΔGint-371 kcal/mol
Surface area53630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.937, 116.937, 218.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-509-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 4 - 270 / Label seq-ID: 24 - 290

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein 3,2-trans-enoyl-CoA isomerase / Delta(3) / Delta(2)-enoyl-CoA isomerase / D3 / D2-enoyl-CoA isomerase / Dodecenoyl-CoA isomerase


Mass: 33965.848 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Cysteine 212 was oxidized to CME (S,S-(2-HYDROXYETHYL)THIOCYSTEINE) in the structure due to the presence of beta-mecarptoethanol.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ECI1, YLR284C / Production host: Escherichia coli (E. coli)
References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES pH 6.5, 1.6 M (NH4)2SO4, 10% dioxane

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 2.14→103.1 Å / Num. obs: 83764 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 14
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k39

1k39


Resolution: 2.14→103.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.219 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19013 4184 5 %RANDOM
Rwork0.16487 ---
obs0.16613 79476 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2---0.25 Å2-0 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Resolution: 2.14→103.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 244 411 6961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196723
X-RAY DIFFRACTIONr_bond_other_d0.0050.026362
X-RAY DIFFRACTIONr_angle_refined_deg1.7172.0069100
X-RAY DIFFRACTIONr_angle_other_deg1.088314664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2455798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71424.585301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.142151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6131529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027443
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021547
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_it2.8273.6953176
X-RAY DIFFRACTIONr_mcbond_other2.8263.6933175
X-RAY DIFFRACTIONr_mcangle_it4.0375.5163967
X-RAY DIFFRACTIONr_mcangle_other4.0375.5183968
X-RAY DIFFRACTIONr_scbond_it4.1894.4153547
X-RAY DIFFRACTIONr_scbond_other4.1894.4153547
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2396.4455130
X-RAY DIFFRACTIONr_long_range_B_refined8.13631.5778045
X-RAY DIFFRACTIONr_long_range_B_other8.13631.5778045
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 / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16342
12B16342
21A16461
22C16461
31B16196
32C16196
LS refinement shellResolution: 2.141→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 290 -
Rwork0.266 5454 -
obs--93.57 %

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