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- PDB-6yh0: Marasmius oreades agglutinin (MOA) in complex with the truncated ... -

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Basic information

Entry
Database: PDB / ID: 6yh0
TitleMarasmius oreades agglutinin (MOA) in complex with the truncated PVPRAHS synthetic substrate
Components
  • Agglutinin
  • PRO-VAL-PRO-ARG
KeywordsTOXIN / fungal chimerolectin / papain-like cysteine protease / protease-substrate complex / calcium-binding protein / manganese-binding protein
Function / homologyAgglutinin, 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 / metal ion binding / Agglutinin
Function and homology information
Biological speciesMarasmius oreades (fairy-ring Marasmius)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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
DepositionMar 28, 2020Deposition 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 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
AAA: Agglutinin
EEE: PRO-VAL-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,59810
Polymers33,1172
Non-polymers1,4818
Water3,657203
1
AAA: Agglutinin
EEE: PRO-VAL-PRO-ARG
hetero molecules

AAA: Agglutinin
EEE: PRO-VAL-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,19620
Polymers66,2354
Non-polymers2,96216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area10170 Å2
ΔGint-56 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.244, 121.244, 99.913
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-579-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AAAEEE

#1: Protein Agglutinin


Mass: 32352.559 Da / Num. of mol.: 1 / Mutation: H257A
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
#2: Protein/peptide PRO-VAL-PRO-ARG


Mass: 764.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Proteolytic peptide substrate / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 3 molecules

#3: 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
#4: Polysaccharide alpha-D-galactopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-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]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 , 4 types, 208 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.27 Å3/Da / Density % sol: 62.44 % / Description: rod-like
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Cacodylate pH 6.5, 0.2 M Sodium acetate, 22% PEG 8000, 10 mM CaCl2, 5 mM DTT
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream on a synchrotron beamline / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972385 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972385 Å / Relative weight: 1
ReflectionResolution: 1.56→105 Å / Num. obs: 61848 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.037 / Rrim(I) all: 0.166 / Net I/σ(I): 12.3
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 15 % / Rmerge(I) obs: 1 / Num. unique obs: 3023 / CC1/2: 0.362 / Rpim(I) all: 1 / Rrim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSMar 15, 2019 BUILT=20190315data reduction
Aimless0.7.4data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 1.56→51.882 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.156 / SU B: 1.49 / SU ML: 0.049 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1993 3149 5.092 %
Rwork0.174 58695 -
all0.175 --
obs-61844 99.981 %
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: 26.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.826 Å20.413 Å20 Å2
2--0.826 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 1.56→51.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 94 203 2605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132560
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182196
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.6973513
X-RAY DIFFRACTIONr_angle_other_deg1.4841.635146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5225320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35123.125128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39115371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8641510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined0.2170.2457
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21938
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21237
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2139
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2990.214
X-RAY DIFFRACTIONr_nbd_other0.1550.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1010.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1030.23
X-RAY DIFFRACTIONr_mcbond_it2.2542.6641210
X-RAY DIFFRACTIONr_mcbond_other2.1792.6631209
X-RAY DIFFRACTIONr_mcangle_it2.9453.9931517
X-RAY DIFFRACTIONr_mcangle_other2.9473.9961518
X-RAY DIFFRACTIONr_scbond_it3.112.9711348
X-RAY DIFFRACTIONr_scbond_other3.1092.9721348
X-RAY DIFFRACTIONr_scangle_it4.5794.3431983
X-RAY DIFFRACTIONr_scangle_other4.554.3451983
X-RAY DIFFRACTIONr_lrange_it5.31851.66310956
X-RAY DIFFRACTIONr_lrange_other5.31751.66310957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.6010.3652230.3644280X-RAY DIFFRACTION99.9778
1.601-1.6440.352320.3374143X-RAY DIFFRACTION99.9543
1.644-1.6920.3292270.34059X-RAY DIFFRACTION100
1.692-1.7440.2922270.2733919X-RAY DIFFRACTION99.9759
1.744-1.8010.2571900.233818X-RAY DIFFRACTION99.9751
1.801-1.8640.2582150.2113696X-RAY DIFFRACTION100
1.864-1.9350.2521820.1943591X-RAY DIFFRACTION99.947
1.935-2.0140.2051680.1823471X-RAY DIFFRACTION100
2.014-2.1030.2171860.1773294X-RAY DIFFRACTION100
2.103-2.2060.1691640.1593193X-RAY DIFFRACTION99.9702
2.206-2.3250.2081580.1573029X-RAY DIFFRACTION100
2.325-2.4660.1931650.1512865X-RAY DIFFRACTION100
2.466-2.6360.1971550.1532700X-RAY DIFFRACTION100
2.636-2.8470.1921520.1662512X-RAY DIFFRACTION100
2.847-3.1190.1521220.1642348X-RAY DIFFRACTION100
3.119-3.4870.1961000.1682153X-RAY DIFFRACTION100
3.487-4.0250.16860.1481916X-RAY DIFFRACTION100
4.025-4.9280.151850.121623X-RAY DIFFRACTION100
4.928-6.9620.174730.1531294X-RAY DIFFRACTION100
6.962-51.8820.177390.191791X-RAY DIFFRACTION99.5204

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