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- PDB-6zrw: Crystal structure of the fungal lectin CML1 -

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Basic information

Entry
Database: PDB / ID: 6zrw
TitleCrystal structure of the fungal lectin CML1
ComponentsMucin-binding lectin 1
KeywordsCARBOHYDRATE / Lectin / fungi / Coprinopsis cinerea
Function / homologycarbohydrate binding / ACETATE ION / : / TRICHLOROPLATINATE / TETRACHLOROPLATINATE(II) / Mucin-binding lectin 1
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsBleuler-Martinez, S. / Olieric, V. / Sharpe, M. / Capitani, G. / Aebi, M. / Kuenzler, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_173097 Switzerland
CitationJournal: Glycobiology / Year: 2022
Title: Structure-function relationship of a novel fucoside-binding fruiting body lectin from Coprinopsis cinerea exhibiting nematotoxic activity.
Authors: Bleuler-Martinez, S. / Varrot, A. / Olieric, V. / Schubert, M. / Vogt, E. / Fetz, C. / Wohlschlager, T. / Plaza, D.F. / Walti, M. / Duport, Y. / Capitani, G. / Aebi, M. / Kunzler, M.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-binding lectin 1
B: Mucin-binding lectin 1
C: Mucin-binding lectin 1
D: Mucin-binding lectin 1
E: Mucin-binding lectin 1
F: Mucin-binding lectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,79251
Polymers81,6856
Non-polymers5,10745
Water15,871881
1
A: Mucin-binding lectin 1
B: Mucin-binding lectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,82514
Polymers27,2282
Non-polymers1,59712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-77 kcal/mol
Surface area10590 Å2
MethodPISA
2
C: Mucin-binding lectin 1
D: Mucin-binding lectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,24820
Polymers27,2282
Non-polymers2,01918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-75 kcal/mol
Surface area10350 Å2
MethodPISA
3
E: Mucin-binding lectin 1
F: Mucin-binding lectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,72017
Polymers27,2282
Non-polymers1,49115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-59 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.497, 73.626, 111.956
Angle α, β, γ (deg.)90.000, 101.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Mucin-binding lectin 1


Mass: 13614.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: cml1 / Production host: Escherichia coli (E. coli) / References: UniProt: B3VS76

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Non-polymers , 6 types, 926 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-P3C / TRICHLOROPLATINATE


Mass: 301.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl3Pt
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PC4 / TETRACHLOROPLATINATE(II)


Mass: 336.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl4Pt
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dehydrate pH 5.6, 30% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0721 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2009
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 1.35→61.17 Å / Num. obs: 303404 / % possible obs: 98.9 % / Redundancy: 7.4 % / CC1/2: 1 / Net I/σ(I): 17.3
Reflection shellResolution: 1.35→1.43 Å / Num. unique obs: 47202 / CC1/2: 0.634

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXDEphasing
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.35→61.17 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.176 7693 5 %
Rwork0.1458 146158 -
obs0.1473 153851 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 287.12 Å2 / Biso mean: 20.7761 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.35→61.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 190 885 6837
Biso mean--63.98 32.49 -
Num. residues----756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.360.3382200.31884160438085
1.36-1.380.31322490.26164724497396
1.38-1.40.29312550.25154846510198
1.4-1.420.26712540.23414821507599
1.42-1.430.26892560.22254893514999
1.43-1.450.27362520.21224773502599
1.45-1.470.26132580.19864903516199
1.47-1.50.23972540.19144838509299
1.5-1.520.22442570.17944868512599
1.52-1.540.19552550.16964846510199
1.54-1.570.2182560.16514872512899
1.57-1.60.19972580.15914916517499
1.6-1.630.19622560.14984857511399
1.63-1.660.18532570.147948745131100
1.66-1.70.19272590.145449235182100
1.7-1.740.18612560.146348695125100
1.74-1.780.19042610.14749575218100
1.78-1.830.18992580.137849055163100
1.83-1.890.15162580.136648935151100
1.89-1.950.20382590.155749305189100
1.95-2.020.1782590.131849105169100
2.02-2.10.16572600.124649375197100
2.1-2.190.15192570.126748955152100
2.19-2.310.22590.14554907516699
2.31-2.450.15452610.12549615222100
2.45-2.640.14782590.125249305189100
2.64-2.910.15642600.129949355195100
2.91-3.330.13482610.121349565217100
3.33-4.190.13622610.121349865247100
4.19-61.170.18082680.163950735341100

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