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- PDB-6lvo: Enoyl-CoA isomerase (BoECI) from Bosea sp. PAMC 26642 -

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Basic information

Entry
Database: PDB / ID: 6lvo
TitleEnoyl-CoA isomerase (BoECI) from Bosea sp. PAMC 26642
ComponentsEnoyl-CoA hydratase
KeywordsISOMERASE / enoyl-CoA
Function / homology
Function and homology information


Enoyl-CoA hydratase, C-terminal / 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
Biological speciesBosea sp. PAMC 26642 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsHwang, J. / Jung, C. / Lee, C.W. / Lee, J.H.
CitationJournal: J.Microbiol / Year: 2020
Title: Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase.
Authors: Hwang, J. / Jeong, C.S. / Lee, C.W. / Shin, S.C. / Kim, H.W. / Lee, S.G. / Youn, U.J. / Lee, C.S. / Oh, T.J. / Kim, H.J. / Park, H. / Park, H.H. / Lee, J.H.
History
DepositionFeb 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)25,3031
Polymers25,3031
Non-polymers00
Water70339
1
A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)75,9103
Polymers75,9103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7200 Å2
ΔGint-47 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.486, 114.486, 114.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

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Components

#1: Protein Enoyl-CoA hydratase /


Mass: 25303.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bosea sp. PAMC 26642 (bacteria) / Gene: AXW83_14375 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A126P0C4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2M zinc acetate, 0.1M imidazole (pH 8.0), 20% (v/v) 1,4-butanediol

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 10379 / % possible obs: 99.9 % / Redundancy: 33.3 % / Biso Wilson estimate: 40.78 Å2 / CC1/2: 1 / Net I/σ(I): 69.8
Reflection shellResolution: 2.35→2.39 Å / Num. unique obs: 521 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fdu

3fdu


Resolution: 2.36→46.74 Å / SU ML: 0.3056 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 31.5905
RfactorNum. reflection% reflection
Rfree0.2769 502 4.84 %
Rwork0.2122 --
obs0.2154 10376 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.24 Å2
Refinement stepCycle: LAST / Resolution: 2.36→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 0 39 1745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941731
X-RAY DIFFRACTIONf_angle_d0.94052346
X-RAY DIFFRACTIONf_chiral_restr0.0481283
X-RAY DIFFRACTIONf_plane_restr0.0053304
X-RAY DIFFRACTIONf_dihedral_angle_d24.4653627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.60.32691350.20572436X-RAY DIFFRACTION100
2.6-2.980.2861330.20672430X-RAY DIFFRACTION100
2.98-3.750.2241100.21892470X-RAY DIFFRACTION99.96
3.75-46.740.2881240.21172538X-RAY DIFFRACTION99.59

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