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- PDB-8id7: Crystal structure of YbiW in complex with 1,5-anhydroglucitol-6-p... -

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Basic information

Entry
Database: PDB / ID: 8id7
TitleCrystal structure of YbiW in complex with 1,5-anhydroglucitol-6-phosphate in Escherichia coli
ComponentsProbable dehydratase YbiW
KeywordsLYASE / glycyl radical enzyme / YbiW / 1 / 5-anhydroglucitol-6-phosphate
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 / : / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
1,5-anhydro-6-O-phosphono-D-glucitol / Probable dehydratase YbiW
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMa, K.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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
DepositionFeb 12, 2023Deposition site: PDBJ / Processing site: PDBC
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)90,3012
Polymers90,0571
Non-polymers2441
Water2,972165
1
A: Probable dehydratase YbiW
hetero molecules

A: Probable dehydratase YbiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,6024
Polymers180,1142
Non-polymers4882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x-1/2,y,-z-1/21
Buried area2530 Å2
ΔGint-16 kcal/mol
Surface area50880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.480, 207.170, 208.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Probable dehydratase YbiW


Mass: 90056.977 Da / Num. of mol.: 1 / Mutation: E114A, E115A, K117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: ybiW, b0823, JW0807 / Production host: Escherichia coli (E. coli)
References: UniProt: P75793, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Sugar ChemComp-0WK / 1,5-anhydro-6-O-phosphono-D-glucitol


Type: D-saccharide / Mass: 244.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
D-1-deoxy-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1M Tris, pH 8.0, 25% (w/v) PEG3350, 10 mM 1,5-anhydroglucitol-6-phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→57.27 Å / Num. obs: 36549 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.085 / Rrim(I) all: 0.211 / Χ2: 0.99 / Net I/σ(I): 7.7 / Num. measured all: 232578
Reflection shellResolution: 2.65→2.72 Å / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.589 / Num. measured all: 18068 / Num. unique obs: 2668 / CC1/2: 0.618 / Rpim(I) all: 0.66 / Rrim(I) all: 1.722 / Χ2: 0.82 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
xia2data reduction
PHENIX1.14refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.482 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1947 5.46 %
Rwork0.2227 --
obs0.226 35659 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→46.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 0 15 165 6444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086411
X-RAY DIFFRACTIONf_angle_d1.0088707
X-RAY DIFFRACTIONf_dihedral_angle_d3.6673826
X-RAY DIFFRACTIONf_chiral_restr0.051972
X-RAY DIFFRACTIONf_plane_restr0.0071140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71630.42321250.35442258X-RAY DIFFRACTION92
2.7163-2.78970.46321260.3492270X-RAY DIFFRACTION94
2.7897-2.87180.40631360.33652284X-RAY DIFFRACTION94
2.8718-2.96450.42631440.31632346X-RAY DIFFRACTION96
2.9645-3.07040.34021360.29582362X-RAY DIFFRACTION96
3.0704-3.19330.38851380.29532394X-RAY DIFFRACTION98
3.1933-3.33860.37381360.27942407X-RAY DIFFRACTION98
3.3386-3.51460.30961450.25592448X-RAY DIFFRACTION99
3.5146-3.73470.28991380.23352439X-RAY DIFFRACTION99
3.7347-4.02290.31380.21322441X-RAY DIFFRACTION99
4.0229-4.42750.23691470.1892487X-RAY DIFFRACTION100
4.4275-5.06750.23541410.172484X-RAY DIFFRACTION100
5.0675-6.38190.22311450.18972496X-RAY DIFFRACTION100
6.3819-46.4820.20981520.16512596X-RAY DIFFRACTION100

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