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- PDB-6zu2: CML1 crystal structure in complex with H-type 1 trisaccharide -

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Basic information

Entry
Database: PDB / ID: 6zu2
TitleCML1 crystal structure in complex with H-type 1 trisaccharide
ComponentsMucin-binding lectin 1
KeywordsSUGAR BINDING PROTEIN / Lectin / fucose binding / hexamer
Function / homologycarbohydrate binding / H type 1 antigen, beta anomer / Mucin-binding lectin 1
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVarrot, A. / Bleuler-Martinez, S.
Funding support France, Switzerland, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-15-IDEX- 02 France
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 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jun 22, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Mucin-binding lectin 1
BBB: Mucin-binding lectin 1
CCC: Mucin-binding lectin 1
DDD: Mucin-binding lectin 1
EEE: Mucin-binding lectin 1
FFF: Mucin-binding lectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,49529
Polymers81,6856
Non-polymers4,81023
Water16,105894
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, VERIFIED BY multi-angle light scattering (MALS), analytical ultracentrifugation (AUC) and sedimentation velocity and small angle X-ray scattering (SAXS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23360 Å2
ΔGint-168 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.040, 74.040, 119.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#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 / Plasmid: pET22b-CML1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3VS76
#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 1 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 894 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.23 % / Description: PARALLEPIPED
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.5 M AmSO4, 100 mM trisodium citrate pH 5.6. Transfer in 2.5 M LI2SO4 for flash freezing in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→37.02 Å / Num. obs: 106704 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.018 / Rrim(I) all: 0.056 / Net I/av σ(I): 6.7 / Net I/σ(I): 21.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.568 / Num. unique obs: 5214 / CC1/2: 0.899 / Rpim(I) all: 0.198 / Rrim(I) all: 0.602 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZRW

6zrw


Resolution: 1.55→37.02 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.285 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.016 / ESU R Free: 0.016
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.181 5401 5.064 %
Rwork0.1505 101249 -
all0.152 --
obs-106650 99.982 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.612 Å2
Baniso -1Baniso -2Baniso -3
1--3.149 Å2-0 Å2-0 Å2
2---3.149 Å2-0 Å2
3---6.298 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 301 894 6970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0136341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175576
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6868725
X-RAY DIFFRACTIONr_angle_other_deg1.5561.61212949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34621.273275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18215894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6411536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021377
X-RAY DIFFRACTIONr_nbd_refined0.1940.21006
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25352
X-RAY DIFFRACTIONr_nbtor_refined0.170.23163
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2533
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.213
X-RAY DIFFRACTIONr_nbd_other0.1950.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.234
X-RAY DIFFRACTIONr_mcbond_it1.8662.0483086
X-RAY DIFFRACTIONr_mcbond_other1.8522.0483085
X-RAY DIFFRACTIONr_mcangle_it2.453.0773870
X-RAY DIFFRACTIONr_mcangle_other2.4523.0773871
X-RAY DIFFRACTIONr_scbond_it2.982.4013255
X-RAY DIFFRACTIONr_scbond_other2.842.3283184
X-RAY DIFFRACTIONr_scangle_it4.2223.514855
X-RAY DIFFRACTIONr_scangle_other4.083.4024748
X-RAY DIFFRACTIONr_lrange_it4.97926.1097105
X-RAY DIFFRACTIONr_lrange_other4.75425.4176937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3054320.2667373X-RAY DIFFRACTION99.8465
1.59-1.6340.2623940.2337265X-RAY DIFFRACTION100
1.634-1.6810.2534380.2137074X-RAY DIFFRACTION100
1.681-1.7330.2513820.1926904X-RAY DIFFRACTION100
1.733-1.7890.2093200.1726674X-RAY DIFFRACTION100
1.789-1.8520.2173520.1726517X-RAY DIFFRACTION100
1.852-1.9220.2142820.1616194X-RAY DIFFRACTION100
1.922-20.2042820.1626135X-RAY DIFFRACTION100
2-2.0880.1743720.1515633X-RAY DIFFRACTION100
2.088-2.190.1793020.1475535X-RAY DIFFRACTION100
2.19-2.3080.172980.1465197X-RAY DIFFRACTION100
2.308-2.4470.1682280.1434963X-RAY DIFFRACTION100
2.447-2.6160.1772210.1464717X-RAY DIFFRACTION100
2.616-2.8240.1662300.1484318X-RAY DIFFRACTION100
2.824-3.0920.1881700.1514022X-RAY DIFFRACTION100
3.092-3.4540.1831750.1443601X-RAY DIFFRACTION100
3.454-3.9820.1491640.1283210X-RAY DIFFRACTION100
3.982-4.8630.1471670.1142666X-RAY DIFFRACTION100
4.863-6.8190.1671140.1432094X-RAY DIFFRACTION99.9547
6.819-37.020.164780.1621157X-RAY DIFFRACTION99.5165

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