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- PDB-1pjh: Structural studies on delta3-delta2-enoyl-CoA isomerase: the vari... -

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Basic information

Entry
Database: PDB / ID: 1pjh
TitleStructural studies on delta3-delta2-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily
Componentsenoyl-CoA isomerase; Eci1p
KeywordsISOMERASE / beta-beta-alpha spiral fold / inter-trimer contacts
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: 2.1 Å
AuthorsMursula, A.M. / Hiltunen, J.K. / Wierenga, R.K.
CitationJournal: Febs Lett. / Year: 2004
Title: Structural studies on delta(3)-delta(2)-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily.
Authors: Mursula, A.M. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: enoyl-CoA isomerase; Eci1p
B: enoyl-CoA isomerase; Eci1p
C: enoyl-CoA isomerase; Eci1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,48417
Polymers95,1553
Non-polymers1,32914
Water6,882382
1
A: enoyl-CoA isomerase; Eci1p
B: enoyl-CoA isomerase; Eci1p
C: enoyl-CoA isomerase; Eci1p
hetero molecules

A: enoyl-CoA isomerase; Eci1p
B: enoyl-CoA isomerase; Eci1p
C: enoyl-CoA isomerase; Eci1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,96834
Polymers190,3106
Non-polymers2,65828
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area28210 Å2
ΔGint-463 kcal/mol
Surface area51420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.243, 116.243, 216.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein enoyl-CoA isomerase; Eci1p


Mass: 31718.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ECI1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLYS(S)
References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 382 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ADA/NaOH, magnesium sulphate, ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1drop
220 mMpotassium phosphate1droppH7.2
3450 mM1dropKCl
41 mMEDTA1drop
51 mMEGTA1drop
60.5 mMbenzamidine HCl1drop
70.1 MADA1reservoirpH7.0
80.1 M1reservoirMgSO4
91.7-2.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.801 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002
RadiationMonochromator: triangular monochromator and bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 86026 / Num. obs: 86026 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.5
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 10.5 / Num. unique all: 10418 / % possible all: 93.4
Reflection
*PLUS
Redundancy: 8 % / Num. measured all: 690091 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
REFMAC5refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNU

1hnu


Resolution: 2.1→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.189 4277 inherit from previous structure
Rwork0.168 --
all0.168 86026 -
obs0.168 86026 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6186 0 74 382 6642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_angle_refined_deg1.21
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 81748 / Num. reflection Rfree: 4278
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.011
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.2

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