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- PDB-8r8a: Structure of the N-terminal domain of CMA in complex with N-acety... -

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Basic information

Entry
Database: PDB / ID: 8r8a
TitleStructure of the N-terminal domain of CMA in complex with N-acetyllactosamine
ComponentsNigrin b-like
KeywordsSUGAR BINDING PROTEIN / lectin / beta-trefoil / galactose / N-acetyllactosamine
Function / homologyRicin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / N-acetyl-alpha-lactosamine / : / Nigrin b-like
Function and homology information
Biological speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.317 Å
AuthorsLundstrom, J. / Varrot, A.
Funding support Sweden, Switzerland, European Union, 4items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Branco Weiss Fellowship - Society in Science Switzerland
COST (European Cooperation in Science and Technology) actionCA18103European Union
COST (European Cooperation in Science and Technology) actionCA18132European Union
CitationJournal: Beilstein J Org Chem / Year: 2024
Title: Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin.
Authors: Lundstrom, J. / Gillon, E. / Chazalet, V. / Kerekes, N. / Di Maio, A. / Feizi, T. / Liu, Y. / Varrot, A. / Bojar, D.
History
DepositionNov 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nigrin b-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6545
Polymers13,9331
Non-polymers7214
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-11 kcal/mol
Surface area6280 Å2
Unit cell
Length a, b, c (Å)36.696, 36.782, 94.786
Angle α, β, γ (deg.)90.000, 99.237, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

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Components

#1: Protein Nigrin b-like


Mass: 13933.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 6-132 of the mature protein preceded by residues left from TEV cleavage site. We used the numbering such as we kept the one of the mature protein
Source: (gene. exp.) Cucumis melo (muskmelon) / Gene: LOC107992255, 107992255 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: A0A1S4E5V9
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.29 Å3/Da / Density % sol: 46.21 % / Description: diamond
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 10% Peg Smear Medium, 0.1 M Mes pH 6.5, and 5 mM of CaCl2, MgCl2, CsCl2, CdCl2, NiCl2 and Zinc acetate transfered in 30% Peg Smear Medium 5mM CdCl2 for cryoprotection

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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: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.317→46.78 Å / Num. obs: 29695 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Net I/σ(I): 25.2
Reflection shellResolution: 1.32→1.34 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 1434 / CC1/2: 0.969 / Rpim(I) all: 0.153 / Rrim(I) all: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.317→46.778 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.297 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions anisotropic refinement
RfactorNum. reflection% reflection
Rfree0.1858 1503 5.062 %
Rwork0.1435 28191 -
all0.146 --
obs-29694 99.798 %
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: 13.471 Å2
Baniso -1Baniso -2Baniso -3
1--0.245 Å2-0 Å2-0.068 Å2
2--0.761 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.317→46.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 29 241 1223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121088
X-RAY DIFFRACTIONr_bond_other_d0.0010.016962
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.7761508
X-RAY DIFFRACTIONr_angle_other_deg0.6161.7492244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.38552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1410159
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0751042
X-RAY DIFFRACTIONr_chiral_restr0.0970.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_nbd_refined0.2130.2193
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.2881
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2551
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2144
X-RAY DIFFRACTIONr_metal_ion_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.220
X-RAY DIFFRACTIONr_nbd_other0.1880.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.236
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2870.22
X-RAY DIFFRACTIONr_mcbond_it4.4451.397558
X-RAY DIFFRACTIONr_mcbond_other4.4441.398558
X-RAY DIFFRACTIONr_mcangle_it5.8522.511709
X-RAY DIFFRACTIONr_mcangle_other5.8522.512710
X-RAY DIFFRACTIONr_scbond_it6.4111.568530
X-RAY DIFFRACTIONr_scbond_other6.4061.57531
X-RAY DIFFRACTIONr_scangle_it8.2832.792798
X-RAY DIFFRACTIONr_scangle_other8.2772.793799
X-RAY DIFFRACTIONr_lrange_it11.38619.7161318
X-RAY DIFFRACTIONr_lrange_other10.26516.7131243
X-RAY DIFFRACTIONr_rigid_bond_restr5.71632050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.317-1.3510.2971200.21620070.2221850.9730.98497.34550.216
1.351-1.3880.1941140.1619900.16221050.9850.99199.95250.16
1.388-1.4280.1831230.13819640.14120870.9810.9911000.138
1.428-1.4720.1771150.12619120.12820270.9840.9921000.126
1.472-1.520.138970.118420.10219390.9880.9941000.1
1.52-1.5730.144850.10218030.10418880.9880.9941000.102
1.573-1.6330.149830.10817280.1118110.9870.9931000.108
1.633-1.6990.154920.11616590.11817510.9880.9921000.116
1.699-1.7750.178770.10316270.10617040.980.9941000.103
1.775-1.8610.135760.1115280.11116040.9880.9931000.11
1.861-1.9620.156670.12114730.12315400.9880.9931000.121
1.962-2.080.151650.12713910.12814560.9880.9921000.127
2.08-2.2240.127790.12712890.12713680.9920.9911000.127
2.224-2.4010.196570.13412100.13612670.9770.9891000.134
2.401-2.630.167680.14111200.14311880.9840.9871000.141
2.63-2.9390.199550.14210060.14410610.9760.9871000.142
2.939-3.3920.195380.1519170.1539550.9740.9851000.151
3.392-4.1480.192430.1637690.1658120.9760.9831000.163
4.148-5.8440.284300.1756030.186330.9670.9861000.175
5.844-46.7780.372190.3143520.3163720.9410.95299.73120.314

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