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- PDB-5zai: Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Meta... -

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Basic information

Entry
Database: PDB / ID: 5zai
TitleCrystal structure of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula
Components3-hydroxypropionyl-coenzyme A dehydratase
KeywordsHYDROLASE
Function / homology
Function and homology information


3-hydroxypropionyl-CoA dehydratase / 3-hydroxypropionyl-CoA dehydratase activity / fatty acid metabolic process
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
COENZYME A / 3-hydroxypropionyl-coenzyme A dehydratase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, D. / Kim, K.J.
CitationJournal: Sci Rep / Year: 2018
Title: Structural Insight into Substrate Specificity of 3-Hydroxypropionyl-Coenzyme A Dehydratase from Metallosphaera sedula
Authors: Lee, D. / Kim, K.J.
History
DepositionFeb 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
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: 3-hydroxypropionyl-coenzyme A dehydratase
B: 3-hydroxypropionyl-coenzyme A dehydratase
C: 3-hydroxypropionyl-coenzyme A dehydratase
D: 3-hydroxypropionyl-coenzyme A dehydratase
E: 3-hydroxypropionyl-coenzyme A dehydratase
F: 3-hydroxypropionyl-coenzyme A dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,79131
Polymers170,1176
Non-polymers4,67425
Water15,313850
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36290 Å2
ΔGint-176 kcal/mol
Surface area50870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.685, 130.170, 84.791
Angle α, β, γ (deg.)90.000, 119.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-hydroxypropionyl-coenzyme A dehydratase / 3-hydroxypropionyl-CoA dehydratase


Mass: 28352.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (archaea) / Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_2001 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_T1R(DE3)
References: UniProt: A4YI89, 3-hydroxypropionyl-CoA dehydratase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10%(w/v) polyethylene glycol (PEG) 8000, 0.1M Sodium-potassium phosphate, pH 6.2, 0.2M Sodium Chloride, 10mM Ethylenediaminetetraacetic acid (EDTA) disodium salt dehydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2017
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: 1.8→73.75 Å / Num. obs: 138405 / % possible obs: 98.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Net I/σ(I): 30.4
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.359 / Num. unique obs: 12686 / Rpim(I) all: 0.202

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZK

3pzk


Resolution: 1.8→25.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.129 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 7078 4.9 %RANDOM
Rwork0.1833 ---
obs0.1856 138405 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.76 Å2 / Biso mean: 26.948 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-1.35 Å2
2---0.43 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.8→25.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11867 0 296 850 13013
Biso mean--54.63 33.41 -
Num. residues----1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01412399
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711948
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.68616685
X-RAY DIFFRACTIONr_angle_other_deg0.9181.66128027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38151553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35222.539571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.814152339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9481584
X-RAY DIFFRACTIONr_chiral_restr0.1010.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213593
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022055
LS refinement shellResolution: 1.796→1.843 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 494 -
Rwork0.327 9579 -
all-10073 -
obs--91.54 %

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