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- PDB-1hnu: CRYSTAL STRUCTURE OF PEROXISOMAL DELTA3-DELTA2-ENOYL-COA ISOMERAS... -

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Basic information

Entry
Database: PDB / ID: 1hnu
TitleCRYSTAL STRUCTURE OF PEROXISOMAL DELTA3-DELTA2-ENOYL-COA ISOMERASE FROM SACCHAROMYCES CEREVISIAE
ComponentsD3,D2-ENOYL COA ISOMERASE ECI1
KeywordsISOMERASE / alpha/beta
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
PERRHENATE / 3,2-trans-enoyl-CoA isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsMursula, A.M. / van Aalten, D.M.F. / Hiltunen, J.K. / Wierenga, R.K.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase.
Authors: Mursula, A.M. / van Aalten, D.M. / Hiltunen, J.K. / Wierenga, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and X-ray Diffraction Analysis of Peroxisomal delta3-delta2-enoyl-CoA Isomerase from Saccharomyces cerevisiae
Authors: Mursula, A.M. / van Aalten, D.M. / Modis, Y. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionDec 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D3,D2-ENOYL COA ISOMERASE ECI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3435
Polymers31,7181
Non-polymers6254
Water3,495194
1
A: D3,D2-ENOYL COA ISOMERASE ECI1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)194,05730
Polymers190,3106
Non-polymers3,74724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
2
A: D3,D2-ENOYL COA ISOMERASE ECI1
hetero molecules

A: D3,D2-ENOYL COA ISOMERASE ECI1
hetero molecules

A: D3,D2-ENOYL COA ISOMERASE ECI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,02915
Polymers95,1553
Non-polymers1,87412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10470 Å2
ΔGint-49 kcal/mol
Surface area28940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.139, 116.139, 123.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

21A-729-

HOH

31A-793-

HOH

41A-795-

HOH

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Components

#1: Protein D3,D2-ENOYL COA ISOMERASE ECI1


Mass: 31718.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-REO / PERRHENATE


Mass: 250.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O4Re
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MES, ammonium sulfate, 1,4-dioxane, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMES11
25 %(w/v)1,4-dioxane11
31.4 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.1765, 1.1773, 1.1697, 1.1836
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 1999
RadiationMonochromator: synchrotron / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.17651
21.17731
31.16971
41.18361
ReflectionResolution: 2.15→30 Å / Num. all: 27191 / Num. obs: 27191 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 40.97 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2651 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 2651

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.15→20 Å / Isotropic thermal model: individual isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 1347 random
Rwork0.215 --
all0.215 26907 -
obs0.215 26907 -
Displacement parametersBiso mean: 44.95 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 18 194 2189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_mcbond_it4.182
LS refinement shellResolution: 2.15→2.25 Å
RfactorNum. reflection
Rfree0.29 169
Rwork0.226 -
obs-3217
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.7

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