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- PDB-2dub: ENOYL-COA HYDRATASE COMPLEXED WITH OCTANOYL-COA -

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Basic information

Entry
Database: PDB / ID: 2dub
TitleENOYL-COA HYDRATASE COMPLEXED WITH OCTANOYL-COA
Components2-ENOYL-COA HYDRATASE
KeywordsLYASE / HYDRATASE / B-OXIDATION / FATTY ACID DEGRADATION / COA / LIGAND BINDING
Function / homology
Function and homology information


Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity ...Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / 3-hydroxypropionyl-CoA dehydratase activity / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of butanoyl-CoA to acetyl-CoA / crotonyl-CoA hydratase activity / Branched-chain amino acid catabolism / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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 ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OCTANOYL-COENZYME A / Enoyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEngel, C.K. / Wierenga, R.K.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The crystal structure of enoyl-CoA hydratase complexed with octanoyl-CoA reveals the structural adaptations required for binding of a long chain fatty acid-CoA molecule.
Authors: Engel, C.K. / Kiema, T.R. / Hiltunen, J.K. / Wierenga, R.K.
#1: Journal: Embo J. / Year: 1996
Title: Crystal Structure of Enoyl-Coenzyme a (Coa) Hydratase at 2.5 Angstroms Resolution: A Spiral Fold Defines the Coa-Binding Pocket
Authors: Engel, C.K. / Mathieu, M. / Zeelen, J.P. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionApr 28, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-ENOYL-COA HYDRATASE
B: 2-ENOYL-COA HYDRATASE
C: 2-ENOYL-COA HYDRATASE
D: 2-ENOYL-COA HYDRATASE
E: 2-ENOYL-COA HYDRATASE
F: 2-ENOYL-COA HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,50410
Polymers169,9296
Non-polymers3,5754
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30860 Å2
ΔGint-191 kcal/mol
Surface area52590 Å2
MethodPISA
2
A: 2-ENOYL-COA HYDRATASE
B: 2-ENOYL-COA HYDRATASE
C: 2-ENOYL-COA HYDRATASE
hetero molecules

D: 2-ENOYL-COA HYDRATASE
E: 2-ENOYL-COA HYDRATASE
F: 2-ENOYL-COA HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,50410
Polymers169,9296
Non-polymers3,5754
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y+1/2,-z+3/21
Buried area33190 Å2
ΔGint-120 kcal/mol
Surface area54650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.240, 93.930, 246.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.372575, -0.459915, 0.806018), (-0.40845, 0.861169, 0.302582), (-0.83328, -0.216484, -0.508703)19.62421, -3.6433, 312.66544
2given(-0.370825, -0.406816, -0.834859), (-0.420558, 0.875056, -0.239601), (0.828021, 0.262257, -0.495582)266.18997, 79.6619, 144.9563
3given(0.506413, 0.450402, 0.735312), (0.444545, -0.867054, 0.224939), (0.738868, 0.212967, -0.639311)-118.39311, 106.17987, 177.82094
4given(-0.984507, -0.002313, 0.175331), (0.003334, -0.999979, 0.005529), (0.175315, 0.006028, 0.984494)118.82172, 184.90572, -11.06223
5given(0.199432, 0.417874, -0.886346), (0.40707, -0.858106, -0.312967), (-0.891359, -0.298389, -0.341237)155.55743, 190.96579, 298.80774

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Components

#1: Protein
2-ENOYL-COA HYDRATASE / CROTONASE / ENOYL-COA HYDRATASE 1


Mass: 28321.514 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: COCRYSTALLIZED WITH OCTANOYL-COA / Source: (natural) Rattus norvegicus (Norway rat) / Cellular location: MITOCHONDRIAMitochondrion / Organ: LIVER / References: UniProt: P14604, enoyl-CoA hydratase
#2: Chemical
ChemComp-CO8 / OCTANOYL-COENZYME A / Octanoyl-CoA


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


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.6 Å3/Da / Density % sol: 53 %
Description: MOLECULAR REPLACEMENT BY RIGID-BODY REFINEMENT IN X-PLOR
Crystal growpH: 7.5
Details: PROTEIN SOLUTION: 4.5 MG/ML PROTEIN IN 20 MM POTASSIUM PHOSPHATE BUFFER, PH 7.2, 3 MM EDTA, 1 MM OCTANOYL-COA RESERVOIR SOLUTION: 2.2 M AMMONIUM SULFATE, 200 MM TRIETHANOLAMINE PH 7.5, 1MM ...Details: PROTEIN SOLUTION: 4.5 MG/ML PROTEIN IN 20 MM POTASSIUM PHOSPHATE BUFFER, PH 7.2, 3 MM EDTA, 1 MM OCTANOYL-COA RESERVOIR SOLUTION: 2.2 M AMMONIUM SULFATE, 200 MM TRIETHANOLAMINE PH 7.5, 1MM DTT, 1MM NAN3, 1MM EDTA, 5% (V/V) N-OCTANOYL CRYSTALS GREW BY MIXING 1 MICROLITER PROTEIN SOLUTION WITH 1 MICROLITER RESERVOIR SOLUTION
PH range: 7.2-7.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.2-2.3 Mammonium salfate1reservoir
2200 mMTEA1reservoir
31 mMdithiothreitol1reservoir
41 mM1reservoirNaN3
51 mMEDTA1reservoir
65 %(v/v)n-octanol1reservoir
72.1-2.15 Mammonium salfate1drop
8100 mMTEA1drop
90.5 mMdithiothreitol1drop
100.5 mM1dropNaN3
112 mMEDTA1drop
122.5 %(v/v)n-octanol1drop
132.25 mg/mlprotein1drop
1410 mMpotassium phosphate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9065
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9065 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 68481 / % possible obs: 99.6 % / Observed criterion σ(I): 4 / Redundancy: 3.95 % / Rsym value: 0.075 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.316 / % possible all: 96
Reflection
*PLUS
Num. obs: 69852 / Num. measured all: 275878 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 96 % / Num. unique obs: 3307 / Rmerge(I) obs: 0.316

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DUB

1dub


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE STRUCTURE WAS REFINED USING THE PROGRAMS X-PLOR AND REFMAC. AFTER STRUCTURE DETERMINATION BY RIGID-BODY REFINEMENT (MODEL: PDB ENTRY 1DUB, WITHOUT LIGAND AND WATER MOLECULES), A SLOW ...Details: THE STRUCTURE WAS REFINED USING THE PROGRAMS X-PLOR AND REFMAC. AFTER STRUCTURE DETERMINATION BY RIGID-BODY REFINEMENT (MODEL: PDB ENTRY 1DUB, WITHOUT LIGAND AND WATER MOLECULES), A SLOW COOL SIMULATED ANNEALING PROTOCOL WAS RUN IN X-PLOR. SUBSEQUENT REFINEMENT WAS DONE WITH REFMAC. FOR BOTH PROGRAMS THE SAME REFLECTIONS WERE USED FOR CROSS VALIDATION. AN X-PLOR BULK SOLVENT CORRECTION WAS USED. AT THE END OF REFINEMENT A POSITIONAL REFINEMENT WAS RUN IN X-PLOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3465 5 %RANDOM
Rwork0.204 ---
obs-68481 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11560 0 228 436 12224
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 68481 / Rfactor obs: 0.204 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_deg1.18

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