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- PDB-6tso: Marasmius oreades agglutinin (MOA) inhibited by cadmium -

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Basic information

Entry
Database: PDB / ID: 6tso
TitleMarasmius oreades agglutinin (MOA) inhibited by cadmium
ComponentsAgglutinin
KeywordsSUGAR BINDING PROTEIN / fungal chimerolectin / papain-like cysteine protease / protease-substrate complex / calcium-binding protein / manganese-binding protein / toxin
Function / homology
Function and homology information


Agglutinin, C-terminal / Agglutinin C-terminal / Ricin-type beta-trefoil lectin domain-like / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesMarasmius oreades (fairy-ring Marasmius)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCordara, G. / Manna, D. / Krengel, U.
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti .
Authors: Manna, D. / Cordara, G. / Krengel, U.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,18410
Polymers32,3291
Non-polymers1,8559
Water1,820101
1
AAA: Agglutinin
hetero molecules

AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,36820
Polymers64,6572
Non-polymers3,71118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area9730 Å2
ΔGint-29 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.752, 120.752, 99.541
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11AAA-491-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Agglutinin


Mass: 32328.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius oreades (fairy-ring Marasmius)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8X123

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2-1/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 107 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylate/HCl pH 6.5, 16% PEG 8000, 0.2 M sodium acetate, 1 mM CdCl2, 10 mM CaCl2, 12.5% DMSO, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 2.0664 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.1→46.3 Å / Num. obs: 44615 / % possible obs: 92.6 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.094 / Rrim(I) all: 0.218 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 1.65 / Num. unique obs: 1659 / CC1/2: 0.518 / Rpim(I) all: 0.818 / Rrim(I) all: 1.85 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDS28-Nov-2019data reduction
XDS28-Nov-2019data scaling
PHASER7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 2.1→46.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.431 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2291 1204 5.017 %
Rwork0.193 --
all0.195 --
obs-23997 92.503 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.886 Å2
Baniso -1Baniso -2Baniso -3
1-1.365 Å20.683 Å20 Å2
2--1.365 Å20 Å2
3----4.428 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 108 101 2487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132489
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182102
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.6893391
X-RAY DIFFRACTIONr_angle_other_deg1.3221.6314900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2255299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24323.74123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.248157
X-RAY DIFFRACTIONr_chiral_restr0.0070.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.2060.2445
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.21966
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21237
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2117
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3080.210
X-RAY DIFFRACTIONr_nbd_other0.1310.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_mcbond_it2.5483.4161181
X-RAY DIFFRACTIONr_mcbond_other2.5463.4161180
X-RAY DIFFRACTIONr_mcangle_it3.2755.111479
X-RAY DIFFRACTIONr_mcangle_other3.2745.1111480
X-RAY DIFFRACTIONr_scbond_it3.0033.6771307
X-RAY DIFFRACTIONr_scbond_other3.0023.6781308
X-RAY DIFFRACTIONr_scangle_it4.3785.4131909
X-RAY DIFFRACTIONr_scangle_other4.3775.4151910
X-RAY DIFFRACTIONr_lrange_it5.56139.9762827
X-RAY DIFFRACTIONr_lrange_other5.55439.9732823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1430.363780.291493X-RAY DIFFRACTION83.8761
2.143-2.2020.294920.2531489X-RAY DIFFRACTION86.252
2.202-2.2650.315900.2331463X-RAY DIFFRACTION87.2962
2.265-2.3350.293680.2321469X-RAY DIFFRACTION88.1307
2.335-2.4120.249690.221421X-RAY DIFFRACTION89.5433
2.412-2.4960.272650.241399X-RAY DIFFRACTION89.5413
2.496-2.590.309710.2011354X-RAY DIFFRACTION90.9381
2.59-2.6960.246810.1891332X-RAY DIFFRACTION92.1722
2.696-2.8160.216680.171297X-RAY DIFFRACTION94.5291
2.816-2.9530.223690.1671273X-RAY DIFFRACTION94.841
2.953-3.1130.246650.1851224X-RAY DIFFRACTION96.482
3.113-3.3020.224680.2011159X-RAY DIFFRACTION97.3037
3.302-3.5290.23630.211112X-RAY DIFFRACTION97.5104
3.529-3.8120.244500.1971056X-RAY DIFFRACTION97.8761
3.812-4.1750.198560.184956X-RAY DIFFRACTION97.2142
4.175-4.6670.182410.144893X-RAY DIFFRACTION98.9407
4.667-5.3870.16370.175806X-RAY DIFFRACTION99.1765
5.387-6.5930.23320.21696X-RAY DIFFRACTION99.4536
6.593-9.3060.205280.165554X-RAY DIFFRACTION98.6441
9.306-46.30.158130.176347X-RAY DIFFRACTION98.3607

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