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- PDB-8r8c: Structure of the N-terminal domain of CMA from Cucumis melo in co... -

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Basic information

Entry
Database: PDB / ID: 8r8c
TitleStructure of the N-terminal domain of CMA from Cucumis melo in complex with N-acetylgalactosamine
ComponentsNigrin b-like
KeywordsSUGAR BINDING PROTEIN / lectin / beta-trefoil / galactose / N-acetyllactosamine
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / : / 2-acetamido-2-deoxy-beta-D-galactopyranose / Nigrin b-like
Similarity search - Component
Biological speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVarrot, A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Other government
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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nigrin b-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7136
Polymers13,9331
Non-polymers7805
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-4 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.613, 36.860, 94.813
Angle α, β, γ (deg.)90.000, 99.166, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-456-

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
Source: (gene. exp.) Cucumis melo (muskmelon) / Gene: LOC107992255, 107992255 / Variant: makuva / Plasmid: pET40b-TEV-cma-Nter / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: A0A1S4E5V9
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.93 % / Description: diamond
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% Peg Smear Medium 0.1M Mes pH 6.5 5 mM of CaCl2, MgCl2, CsCl2, CdCl2, NiCl2 and Zinc acetate and GalNAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.55→35.68 Å / Num. obs: 18279 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.037 / Rrim(I) all: 0.064 / Net I/σ(I): 14.4
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4581 / CC1/2: 0.857 / Rpim(I) all: 0.364 / Rrim(I) all: 0.618

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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: 1.55→35.68 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.527 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.204 905 4.951 %
Rwork0.1629 17373 -
all0.165 --
obs-18278 99.667 %
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: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.871 Å20 Å20.034 Å2
2--1.355 Å20 Å2
3----0.471 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 33 171 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121043
X-RAY DIFFRACTIONr_bond_other_d0.0010.016916
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.7751439
X-RAY DIFFRACTIONr_angle_other_deg0.6691.7462128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.25952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82110147
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8371041
X-RAY DIFFRACTIONr_chiral_restr0.0920.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2070.2185
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.2870
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2528
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.2537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2118
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.211
X-RAY DIFFRACTIONr_nbd_other0.180.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1230.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1030.22
X-RAY DIFFRACTIONr_mcbond_it2.1091.849530
X-RAY DIFFRACTIONr_mcbond_other2.1041.849530
X-RAY DIFFRACTIONr_mcangle_it3.0253.317666
X-RAY DIFFRACTIONr_mcangle_other3.0233.318667
X-RAY DIFFRACTIONr_scbond_it3.1512.044513
X-RAY DIFFRACTIONr_scbond_other3.1482.045514
X-RAY DIFFRACTIONr_scangle_it4.6083.628773
X-RAY DIFFRACTIONr_scangle_other4.6053.628774
X-RAY DIFFRACTIONr_lrange_it5.65822.3531212
X-RAY DIFFRACTIONr_lrange_other5.61521.0721171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.283600.2811288X-RAY DIFFRACTION99.7041
1.59-1.6340.293660.2481233X-RAY DIFFRACTION99.8463
1.634-1.6810.248550.1971228X-RAY DIFFRACTION99.8444
1.681-1.7330.197700.1521156X-RAY DIFFRACTION100
1.733-1.7890.205610.1431142X-RAY DIFFRACTION99.9169
1.789-1.8520.19570.1461098X-RAY DIFFRACTION99.8271
1.852-1.9220.226650.1461068X-RAY DIFFRACTION99.9118
1.922-20.183510.1611012X-RAY DIFFRACTION99.8122
2-2.0880.208420.157991X-RAY DIFFRACTION99.6143
2.088-2.190.198530.152927X-RAY DIFFRACTION99.4924
2.19-2.3080.208520.152905X-RAY DIFFRACTION99.7915
2.308-2.4470.206490.142849X-RAY DIFFRACTION99.5565
2.447-2.6150.157410.154792X-RAY DIFFRACTION99.7605
2.615-2.8240.241380.154756X-RAY DIFFRACTION99.25
2.824-3.0910.145390.156667X-RAY DIFFRACTION98.3287
3.091-3.4530.221330.165634X-RAY DIFFRACTION99.8503
3.453-3.9810.222290.163544X-RAY DIFFRACTION99.3068
3.981-4.860.19180.143477X-RAY DIFFRACTION99.3976
4.86-6.8110.198140.196380X-RAY DIFFRACTION99.4949
6.811-35.680.198120.191225X-RAY DIFFRACTION99.5798

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