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- PDB-8yjn: Structure of E. coli glycyl radical enzyme YbiW with bound glycerol -

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Basic information

Entry
Database: PDB / ID: 8yjn
TitleStructure of E. coli glycyl radical enzyme YbiW with bound glycerol
ComponentsProbable dehydratase YbiW
KeywordsLYASE / Glycyl radical enzyme
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / lyase activity / cytosol
Similarity search - Function
Glycyl radical enzyme, PFL2/glycerol dehydratase family / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
Probable dehydratase YbiW
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsXue, B. / Wei, Y. / Robinson, R.C. / Yew, W.S. / Zhang, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: A Widespread Radical-Mediated Glycolysis Pathway.
Authors: Ma, K. / Xue, B. / Chu, R. / Zheng, Y. / Sharma, S. / Jiang, L. / Hu, M. / Xie, Y. / Hu, Y. / Tao, T. / Zhou, Y. / Liu, D. / Li, Z. / Yang, Q. / Chen, Y. / Wu, S. / Tong, Y. / Robinson, R.C. ...Authors: Ma, K. / Xue, B. / Chu, R. / Zheng, Y. / Sharma, S. / Jiang, L. / Hu, M. / Xie, Y. / Hu, Y. / Tao, T. / Zhou, Y. / Liu, D. / Li, Z. / Yang, Q. / Chen, Y. / Wu, S. / Tong, Y. / Robinson, R.C. / Yew, W.S. / Jin, X. / Liu, Y. / Zhao, H. / Ang, E.L. / Wei, Y. / Zhang, Y.
History
DepositionMar 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable dehydratase YbiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8442
Polymers91,7521
Non-polymers921
Water6,467359
1
A: Probable dehydratase YbiW
hetero molecules

A: Probable dehydratase YbiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,6884
Polymers183,5032
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area50200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.926, 207.040, 210.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1339-

HOH

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Components

#1: Protein Probable dehydratase YbiW


Mass: 91751.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ybiW, b0823, JW0807 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P75793, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Imidazole pH 8.0, 1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.42→46.95 Å / Num. obs: 47693 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Net I/σ(I): 16.9 / Num. measured all: 358154
Reflection shellResolution: 2.42→2.51 Å / % possible obs: 99.3 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.495 / Num. measured all: 34768 / Num. unique obs: 4632 / CC1/2: 0.945 / Rpim(I) all: 0.193 / Rrim(I) all: 0.531 / Net I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→38.84 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 2360 4.95 %
Rwork0.1737 --
obs0.1756 47675 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6314 0 6 359 6679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076451
X-RAY DIFFRACTIONf_angle_d0.8688750
X-RAY DIFFRACTIONf_dihedral_angle_d5.879882
X-RAY DIFFRACTIONf_chiral_restr0.051969
X-RAY DIFFRACTIONf_plane_restr0.0081149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.470.32421280.2482619X-RAY DIFFRACTION98
2.47-2.520.26971310.21262633X-RAY DIFFRACTION100
2.52-2.580.25321290.21062651X-RAY DIFFRACTION100
2.58-2.650.27821430.222647X-RAY DIFFRACTION100
2.65-2.720.25441330.20772646X-RAY DIFFRACTION100
2.72-2.80.25721510.20592646X-RAY DIFFRACTION100
2.8-2.890.23241710.19872596X-RAY DIFFRACTION100
2.89-2.990.28841420.19882651X-RAY DIFFRACTION100
2.99-3.110.23861480.18882652X-RAY DIFFRACTION100
3.11-3.250.26711330.20222649X-RAY DIFFRACTION100
3.25-3.430.23531370.2012673X-RAY DIFFRACTION100
3.43-3.640.20821300.17092671X-RAY DIFFRACTION100
3.64-3.920.17151450.16222659X-RAY DIFFRACTION100
3.92-4.320.17291440.14162679X-RAY DIFFRACTION100
4.32-4.940.15591220.13342728X-RAY DIFFRACTION100
4.94-6.220.19261450.16242696X-RAY DIFFRACTION100
6.22-38.840.18891280.14882819X-RAY DIFFRACTION100

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