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- PDB-1k39: The structure of yeast delta3-delta2-enoyl-COA isomerase complexe... -

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Basic information

Entry
Database: PDB / ID: 1k39
TitleThe structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA
Componentsd3,d2-enoyl CoA isomerase ECI1
KeywordsISOMERASE / beta-beta-alpha spiral
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
OCTANOYL-COENZYME A / PHOSPHATE ION / 3,2-trans-enoyl-CoA isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsMursula, A.M. / Geerlof, A. / Hiltunen, J.K. / Wierenga, R.K.
Citation
#1: Journal: J.Mol.Biol. / Year: 2001
Title: The crystal structure of delta3-delta2-enoyl-CoA isomerase
Authors: Mursula, A.M. / van Aalten, D.M.F. / Hiltunen, J.K. / Wierenga, R.K.
#2: 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.F. / Modis, Y. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _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: d3,d2-enoyl CoA isomerase ECI1
B: d3,d2-enoyl CoA isomerase ECI1
C: d3,d2-enoyl CoA isomerase ECI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1219
Polymers95,1553
Non-polymers2,9666
Water362
1
A: d3,d2-enoyl CoA isomerase ECI1
B: d3,d2-enoyl CoA isomerase ECI1
C: d3,d2-enoyl CoA isomerase ECI1
hetero molecules

A: d3,d2-enoyl CoA isomerase ECI1
B: d3,d2-enoyl CoA isomerase ECI1
C: d3,d2-enoyl CoA isomerase ECI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,24218
Polymers190,3106
Non-polymers5,93212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area30410 Å2
ΔGint-119 kcal/mol
Surface area54970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.650, 116.650, 216.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit.

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Components

#1: Protein d3,d2-enoyl CoA isomerase ECI1


Mass: 31718.369 Da / Num. of mol.: 3 / Mutation: M25I
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): BL21(DE3)pLysS
References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CO8 / OCTANOYL-COENZYME A


Mass: 893.730 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H50N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M TEA, 1.3 M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.946 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 2000
RadiationMonochromator: bendable mirror and asymmetrically cut Si(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 23549 / Num. obs: 22527 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.5
Reflection shellResolution: 3.3→3.42 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
REFMAC5.1.24refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNU

1hnu


Resolution: 3.29→20 Å / SU B: 17.906 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26209 1162 5.1 %RANDOM
Rwork0.20508 ---
obs0.208 21512 96.9 %-
all-21372 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 3.29→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 186 2 6587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226565
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9938881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024858
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.23473
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.451.53894
X-RAY DIFFRACTIONr_mcangle_it0.88726274
X-RAY DIFFRACTIONr_scbond_it1.18632671
X-RAY DIFFRACTIONr_scangle_it2.0974.52607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.286→3.369 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 81
Rwork0.206 1405
Refinement TLS params.Method: refined / Origin x: -11.499 Å / Origin y: 10.513 Å / Origin z: 146.123 Å
111213212223313233
T0.0998 Å20.024 Å2-0.0093 Å2-0.0274 Å2-0.0275 Å2--0.0305 Å2
L0.6581 °20.1307 °20.2975 °2-1.0919 °20.23 °2--1.1005 °2
S0.0233 Å °0.1352 Å °-0.0347 Å °-0.286 Å °0.0387 Å °-0.0518 Å °0.0418 Å °0.1938 Å °-0.062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2724 - 272
2X-RAY DIFFRACTION1BB4 - 2744 - 274
3X-RAY DIFFRACTION1CC5 - 2705 - 270

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