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- PDB-5v6j: Glycan binding protein Y3 from mushroom Coprinus comatus possesse... -

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Basic information

Entry
Database: PDB / ID: 5v6j
TitleGlycan binding protein Y3 from mushroom Coprinus comatus possesses anti-leukemic activity
ComponentsTMV resistance protein Y3
KeywordsSUGAR BINDING PROTEIN / Glycan binding protein / Lectin
Function / homologyTMV resistance protein Y3
Function and homology information
Biological speciesCoprinus comatus (shaggy mane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 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.
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: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
C: TMV resistance protein Y3
D: TMV resistance protein Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7318
Polymers48,9024
Non-polymers8294
Water12,917717
1
A: TMV resistance protein Y3
B: TMV resistance protein Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8664
Polymers24,4512
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TMV resistance protein Y3
D: TMV resistance protein Y3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8664
Polymers24,4512
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.265, 56.098, 62.728
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TMV resistance protein Y3 / Y3 protein


Mass: 12225.509 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 1.95 Å3/Da / Density % sol: 35.97 %
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-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2014
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.179→41.795 Å / Num. obs: 113409 / % possible obs: 90 % / Redundancy: 5 % / Rmerge(I) obs: 0.04129 / Rsym value: 0.04611 / Net I/σ(I): 22.98
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.2976 / Mean I/σ(I) obs: 4.4 / % possible all: 80

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: SAD / Resolution: 1.18→41.795 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
RfactorNum. reflection% reflection
Rfree0.182 5578 4.92 %
Rwork0.167 --
obs-113405 93.3 %
Solvent computationVDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.18→41.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 52 717 4189

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