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- PDB-6ijk: Enoyl-CoA hydratase/isomerase family protein from Cupriavidus nec... -

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Basic information

Entry
Database: PDB / ID: 6ijk
TitleEnoyl-CoA hydratase/isomerase family protein from Cupriavidus necator H16
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / isomerase
Function / homology: / enoyl-CoA hydratase / Enoyl-CoA hydratase, C-terminal / enoyl-CoA hydratase activity / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / Enoyl-CoA hydratase
Function and homology information
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeo, H. / Kim, K.-J.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016M3D3A1A01913269 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M1A2A2087631 Korea, Republic Of
National Research Foundation (Korea)NRF-2018H1A2A1061751 Korea, Republic Of
CitationJournal: Biotechnol. Bioprocess Eng. / Year: 2019
Title: Crystal structure of a novel type isomerase of enoyl-CoA hydratase/isomerase family protein from Cupriavidus necator H16
Authors: Seo, H. / Kim, K.-J.
History
DepositionOct 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev / _citation.journal_id_ISSN
Revision 1.2Nov 22, 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
B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)64,7192
Polymers64,7192
Non-polymers00
Water84747
1
A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)97,0783
Polymers97,0783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10710 Å2
ΔGint-80 kcal/mol
Surface area29110 Å2
MethodPISA
2
B: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)97,0783
Polymers97,0783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10820 Å2
ΔGint-80 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.941, 132.941, 44.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Enoyl-CoA hydratase


Mass: 32359.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria)
Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: H16_B0756 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0K371, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 550 MME, NaCl, Bicine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 22, 2015
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57392 / % possible obs: 99.3 % / Redundancy: 4.1 % / Rsym value: 0.09 / Net I/σ(I): 41.4
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 8.5 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZAI

5zai


Resolution: 2→35.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.663 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 2887 5 %RANDOM
Rwork0.2025 ---
obs0.204 55042 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.29 Å2 / Biso mean: 33.317 Å2 / Biso min: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å2-0 Å2
2---0.49 Å2-0 Å2
3---1.58 Å2
Refinement stepCycle: final / Resolution: 2→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 0 47 4127
Biso mean---34.96 -
Num. residues----538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173897
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6335663
X-RAY DIFFRACTIONr_angle_other_deg1.4181.5718949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8325536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.14519.737228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01515639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5121544
X-RAY DIFFRACTIONr_chiral_restr0.0860.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 223 -
Rwork0.262 3940 -
all-4163 -
obs--97.15 %

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