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- PDB-5v6i: Glycan binding protein Y3 from mushroom Coprinus comatus possesse... -

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Basic information

Entry
Database: PDB / ID: 5v6i
TitleGlycan binding protein Y3 from mushroom Coprinus comatus possesses anti-leukemic activity - Pt derivative
ComponentsTMV resistance protein Y3
KeywordsSUGAR BINDING PROTEIN / Glycan binding protein / Lectin
Function / homology: / TMV resistance protein Y3
Function and homology information
Biological speciesCoprinus comatus (shaggy mane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLi, K. / Zhang, P. / Gang, Y. / Xia, C. / Polston, J.E. / Li, G. / Li, S. / Lin, Z. / Yang, L.-J. / Bruner, S.D. / Ding, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24 GM098791 United States
University of Florida United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity.
Authors: Zhang, P. / Li, K. / Yang, G. / Xia, C. / Polston, J.E. / Li, G. / Li, S. / Lin, Z. / Yang, L.J. / Bruner, S.D. / Ding, Y.
History
DepositionMar 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 1, 2020Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TMV resistance protein Y3
B: TMV resistance protein Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,07120
Polymers24,4512
Non-polymers1,62018
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-139 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.102, 55.237, 41.879
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimer as determined by gel filtration

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Components

#1: Protein TMV resistance protein Y3 / Y3 protein


Mass: 12225.509 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinus comatus (shaggy mane) / Gene: y3 / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) / References: UniProt: G3BK00
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pt
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.92 Å3/Da / Density % sol: 35.85 % / Description: PLATE-SHAPED CRYSTAL
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 16% PEG4000, 10% V/V GLYCEROL, 0.1 M CHES, PH 9.5 / PH range: 9.5-10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97875 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2015
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 1.699→41.3 Å / Num. obs: 20217 / % possible obs: 99 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.0928 / Net I/σ(I): 14.57
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4428 / % possible all: 87

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→41.3 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.194 994 4.92 %
Rwork0.16 --
obs0.161 20211 98.7 %
Solvent computationVDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 42 156 1908

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