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- PDB-1dci: DIENOYL-COA ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1dci
TitleDIENOYL-COA ISOMERASE
ComponentsDIENOYL-COA ISOMERASE
KeywordsLYASE / DIENOYL-COA ISOMERASE
Function / homology
Function and homology information


delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity / Peroxisomal protein import / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / fatty acid beta-oxidation / peroxisome / 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
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.5 Å
AuthorsModis, Y. / Filppula, S.A. / Novikov, D. / Norledge, B. / Hiltunen, J.K. / Wierenga, R.K.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis.
Authors: Modis, Y. / Filppula, S.A. / Novikov, D.K. / Norledge, B. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionFeb 13, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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: DIENOYL-COA ISOMERASE
B: DIENOYL-COA ISOMERASE
C: DIENOYL-COA ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,54822
Polymers91,2483
Non-polymers1,30019
Water17,529973
1
A: DIENOYL-COA ISOMERASE
B: DIENOYL-COA ISOMERASE
C: DIENOYL-COA ISOMERASE
hetero molecules

A: DIENOYL-COA ISOMERASE
B: DIENOYL-COA ISOMERASE
C: DIENOYL-COA ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,09744
Polymers182,4966
Non-polymers2,60038
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area37960 Å2
ΔGint-321 kcal/mol
Surface area51800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.543, 131.543, 96.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-18-

MG

21A-353-

HOH

31C-643-

HOH

41C-646-

HOH

51C-649-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.456903, 0.875078, -0.159382), (-0.823899, -0.483866, -0.2949), (-0.33521, -0.003433, 0.942089)127.23271, 152.50018, 37.636
2given(-0.45743, -0.825448, -0.330637), (0.87453, -0.484863, -0.000522), (-0.160751, -0.288916, 0.94371)196.44098, -37.28777, 29.79203

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Components

#1: Protein DIENOYL-COA ISOMERASE / DELTA3 / 5 / DELTA2 / 4-DIENOYL-COENZYME A ISOMERASE / PROBABLE PEROXISOMAL ENOYL-COA HYDRATASE


Mass: 30416.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: WISTAR / Cell line: BL21 / Cellular location: PEROXISOME, MITOCHONDRIA / Organ: LIVER / Organelle: PEROXISOME, MITOCHONDRIA / Plasmid: PET3A (NOVAGEN) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: Q62651, enoyl-CoA hydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 973 / 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: 50 %
Crystal growpH: 8.75 / Details: pH 8.75
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 mg/mlprotein1drop
225 mMpotassium phosphate1drop
3100 mMsodium chloride1drop
41 mMdithiothreitol1drop
51 mMEDTA1drop
61 mMsodium azide1drop
71.75 Mmagnesium sulphate1reservoir
8100 mMTris-hydroxymethyl-amino methane hydrochloride1reservoir
92 %(v/v)ethylene glycol1reservoir
101 mMdithiothreitol1reservoir
111 mMEDTA1reservoir
121 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9092
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: BENT MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9092 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 153741 / % possible obs: 94.1 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.6
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.7 / % possible all: 84
Reflection shell
*PLUS
% possible obs: 84.3 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 7231 5 %RANDOM
Rwork0.176 ---
obs-144296 93.9 %-
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.513 Å22.513 Å20 Å2
2--0 Å21.988 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6375 0 72 973 7420
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.025
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8185
X-RAY DIFFRACTIONp_mcangle_it2.1834
X-RAY DIFFRACTIONp_scbond_it2.6425
X-RAY DIFFRACTIONp_scangle_it3.6266
X-RAY DIFFRACTIONp_plane_restr0.020.289
X-RAY DIFFRACTIONp_chiral_restr0.1060.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1570.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1570.3
X-RAY DIFFRACTIONp_planar_tor4.33
X-RAY DIFFRACTIONp_staggered_tor16.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.320
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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