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- PDB-4zdf: Crystal structure of yeast enoyl-CoA isomerase helix-10 deletion ... -

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Basic information

Entry
Database: PDB / ID: 4zdf
TitleCrystal structure of yeast enoyl-CoA isomerase helix-10 deletion (ScECI2-H10) mutant
Components3,2-trans-enoyl-CoA isomerase
KeywordsISOMERASE / Crotonase / enoyl-CoA isomerase / 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
3,2-trans-enoyl-CoA isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsOnwukwe, G.U. / Koski, M.K. / Wierenga, R.K.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,0343
Polymers64,9422
Non-polymers921
Water5,495305
1
A: 3,2-trans-enoyl-CoA isomerase
B: 3,2-trans-enoyl-CoA isomerase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)195,1039
Polymers194,8266
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_895-y+3,x-y+4,z1
crystal symmetry operation3_485-x+y-1,-x+3,z1
Buried area22360 Å2
ΔGint-141 kcal/mol
Surface area53700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.121, 118.121, 87.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-266-

LYS

21A-541-

HOH

31B-428-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 4 - 267 / Label seq-ID: 24 - 287

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 32471.053 Da / Num. of mol.: 2 / Mutation: Deleted R269-L280
Source method: isolated from a genetically manipulated source
Details: CYS212 was oxidized to CME due to the presence of BME in the purification buffers
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ECI1, YLR284C / Production host: Escherichia coli (E. coli)
References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.7 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM imidazole pH 6.5, 1 M NaAcetate

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS 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: 1.81→48.94 Å / Num. obs: 64106 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.3
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.064 / Mean I/σ(I) obs: 1.6 / % possible all: 97.2

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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: 1.81→48.94 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.428 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18785 3239 5.1 %RANDOM
Rwork0.15917 ---
obs0.16062 60869 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---2.15 Å2
Refinement stepCycle: 1 / Resolution: 1.81→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 6 305 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194271
X-RAY DIFFRACTIONr_bond_other_d0.0040.024080
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.975782
X-RAY DIFFRACTIONr_angle_other_deg0.99239416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00524.694196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2115750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841518
X-RAY DIFFRACTIONr_chiral_restr0.0980.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024859
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02991
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_it2.4973.2262095
X-RAY DIFFRACTIONr_mcbond_other2.4973.2252094
X-RAY DIFFRACTIONr_mcangle_it3.6984.8112631
X-RAY DIFFRACTIONr_mcangle_other3.6974.8122632
X-RAY DIFFRACTIONr_scbond_it3.6743.7612176
X-RAY DIFFRACTIONr_scbond_other3.6563.7612176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7715.4243152
X-RAY DIFFRACTIONr_long_range_B_refined9.326.9975040
X-RAY DIFFRACTIONr_long_range_B_other9.30227.0045041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15394 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 247 -
Rwork0.299 4296 -
obs--96.15 %

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