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- PDB-6tsq: Marasmius oreades agglutinin (MOA) activated by manganese (II) -

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Basic information

Entry
Database: PDB / ID: 6tsq
TitleMarasmius oreades agglutinin (MOA) activated by manganese (II)
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: 1.85 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 21, 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
Revision 1.3Oct 9, 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
AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,33813
Polymers32,4201
Non-polymers1,91812
Water4,071226
1
AAA: Agglutinin
hetero molecules

AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,67626
Polymers64,8392
Non-polymers3,83724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area11090 Å2
ΔGint-17 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.952, 120.952, 99.477
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-4-

ARG

21AAA-594-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Agglutinin


Mass: 32419.629 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 , 6 types, 235 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 62.5 %
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, 0.15M sodium acetate, 5 mM MnCl2, 12.5% DMSO, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.85051 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85051 Å / Relative weight: 1
ReflectionResolution: 1.85→46.3 Å / Num. obs: 63674 / % possible obs: 90.2 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 22.8
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.256 / Num. unique obs: 1262 / CC1/2: 0.853 / Rpim(I) all: 0.256 / Rrim(I) all: 0.361 / % possible all: 57.8

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDSSeptember 26, 2012data reduction
XDSSeptember 26, 2012data scaling
PHASER7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 1.85→46.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.768 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1824 1728 5.009 %
Rwork0.1558 --
all0.157 --
obs-34498 93.137 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.957 Å2
Baniso -1Baniso -2Baniso -3
1-0.518 Å20.259 Å20 Å2
2--0.518 Å20 Å2
3----1.679 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 117 226 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132586
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182201
X-RAY DIFFRACTIONr_angle_refined_deg0.8151.6923537
X-RAY DIFFRACTIONr_angle_other_deg0.6061.635145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8145323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32423.721129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52115366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.317158
X-RAY DIFFRACTIONr_chiral_restr0.0120.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.022891
X-RAY DIFFRACTIONr_gen_planes_other0.0340.02557
X-RAY DIFFRACTIONr_nbd_refined0.2510.2470
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22032
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21271
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1040.21144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2173
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.7960.21
X-RAY DIFFRACTIONr_metal_ion_refined0.3510.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2630.217
X-RAY DIFFRACTIONr_nbd_other0.2350.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4820.22
X-RAY DIFFRACTIONr_mcbond_it1.3571.7571217
X-RAY DIFFRACTIONr_mcbond_other1.3571.7571216
X-RAY DIFFRACTIONr_mcangle_it1.8262.631532
X-RAY DIFFRACTIONr_mcangle_other1.8262.631533
X-RAY DIFFRACTIONr_scbond_it2.0651.9821369
X-RAY DIFFRACTIONr_scbond_other2.0651.9821370
X-RAY DIFFRACTIONr_scangle_it3.1362.8881994
X-RAY DIFFRACTIONr_scangle_other3.1352.8881995
X-RAY DIFFRACTIONr_lrange_it4.11721.2882998
X-RAY DIFFRACTIONr_lrange_other4.03721.0582960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.238880.2221461X-RAY DIFFRACTION57.8633
1.9-1.9520.23950.1881818X-RAY DIFFRACTION72.2705
1.952-2.0080.2041130.162066X-RAY DIFFRACTION85.8888
2.008-2.070.1871200.1532244X-RAY DIFFRACTION95.7085
2.07-2.1380.1821190.1432246X-RAY DIFFRACTION98.5827
2.138-2.2130.171120.1412182X-RAY DIFFRACTION98.118
2.213-2.2960.2051090.1422139X-RAY DIFFRACTION99.2933
2.296-2.390.1851080.1412018X-RAY DIFFRACTION98.7918
2.39-2.4960.1591110.1351981X-RAY DIFFRACTION99.1939
2.496-2.6180.166880.1381912X-RAY DIFFRACTION99.552
2.618-2.760.173920.1541802X-RAY DIFFRACTION99.7893
2.76-2.9270.199860.1591720X-RAY DIFFRACTION99.7239
2.927-3.1290.18870.1541621X-RAY DIFFRACTION99.9415
3.129-3.3790.193870.1711505X-RAY DIFFRACTION99.8119
3.379-3.7010.211750.1671411X-RAY DIFFRACTION100
3.701-4.1380.155720.1531286X-RAY DIFFRACTION99.8529
4.138-4.7770.13420.131155X-RAY DIFFRACTION99.8332
4.777-5.8470.184600.164976X-RAY DIFFRACTION99.9036
5.847-8.2560.179430.204787X-RAY DIFFRACTION99.8797
8.256-46.30.189210.185440X-RAY DIFFRACTION90.0391

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