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- PDB-1xx4: Crystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 1xx4
TitleCrystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA
Components3,2-trans-enoyl-CoA isomerase, mitochondrial
KeywordsISOMERASE / crotonase superfamily / domain swapped
Function / homology
Function and homology information


mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / Mitochondrial protein degradation / intramolecular oxidoreductase activity, transposing C=C bonds / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / fatty acid beta-oxidation / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / PHOSPHATE ION / Enoyl-CoA delta isomerase 1, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHubbard, P.A. / Yu, W. / Schulz, H. / Kim, J.-J.
CitationJournal: Protein Sci. / Year: 2005
Title: Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase.
Authors: Hubbard, P.A. / Yu, W. / Schulz, H. / Kim, J.J.
History
DepositionNov 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THE AUTHORS STATE THAT ELECTRON DENSITIES AND FINAL MODEL AT RESIDUES 61 AND 101 DO NOT ...SEQUENCE THE AUTHORS STATE THAT ELECTRON DENSITIES AND FINAL MODEL AT RESIDUES 61 AND 101 DO NOT AGREE WITH THE CORRESPONDING SWISSPROT ENTRY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,20310
Polymers29,3611
Non-polymers8429
Water1,62190
1
A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules

A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules

A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,60830
Polymers88,0833
Non-polymers2,52527
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
MethodPQS
2
A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules

A: 3,2-trans-enoyl-CoA isomerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,40520
Polymers58,7222
Non-polymers1,68318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation43_655-x+5/4,-z+1/4,-y+1/41
Buried area3620 Å2
ΔGint-236 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.918, 169.918, 169.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-575-

HOH

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Components

#1: Protein 3,2-trans-enoyl-CoA isomerase, mitochondrial / Dodecenoyl-CoA delta-isomerase


Mass: 29360.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dci / Plasmid: pND-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P23965, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG-MME 550, MES, zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceTypeID
ROTATING ANODERIGAKU RU3001
ROTATING ANODERIGAKU RU2002
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATENov 3, 2003Osmic confocal mirrors
RIGAKU RAXIS IIC2IMAGE PLATEOct 14, 2003osmic confocal mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic confocal mirrorsSINGLE WAVELENGTHMx-ray1
2Osmic confocal mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→29.15 Å / Num. all: 21528 / Num. obs: 21510 / % possible obs: 99.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2.2 / Redundancy: 19.76 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2108 / Rsym value: 0.411 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL OF CROTONASE FOLD

Resolution: 2.2→29.15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 255422.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1052 5 %RANDOM
Rwork0.239 ---
obs0.245 21506 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3253 Å2 / ksol: 0.361821 e/Å3
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 45 90 2141
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 168 5.3 %
Rwork0.351 3349 -
obs-6720 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.ROP
X-RAY DIFFRACTION4PO4.PARAMPO4.TOP
X-RAY DIFFRACTION5bam.parambam.top

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