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- PDB-6tsn: Marasmius oreades agglutinin (MOA), papain back.swap W208Q-Q276W ... -

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Basic information

Entry
Database: PDB / ID: 6tsn
TitleMarasmius oreades agglutinin (MOA), papain back.swap W208Q-Q276W variant
ComponentsAgglutinin
KeywordsSUGAR BINDING PROTEIN / fungal chimerolectin / papain-like cysteine protease / protease-substrate complex / calcium-binding protein / manganese-binding protein / toxin
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Revision 1.3Oct 16, 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)34,1289
Polymers32,4201
Non-polymers1,7098
Water3,549197
1
AAA: Agglutinin
hetero molecules

AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,25718
Polymers64,8392
Non-polymers3,41716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area9460 Å2
ΔGint-2 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.615, 121.615, 100.032
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-567-

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.: 2
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.: 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 , 5 types, 202 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.3 Å3/Da / Density % sol: 63.2 % / Description: rod-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylate/HCl pH 6.5, 14% PEG 8000, 0.2 M calcium acetate, 10% DMSO, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→46.6 Å / Num. obs: 104686 / % possible obs: 94.8 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.051 / Rrim(I) all: 0.145 / Net I/σ(I): 14.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.749 / Num. unique obs: 2154 / CC1/2: 0.265 / Rpim(I) all: 1.572 / Rrim(I) all: 2.359 / % possible all: 77.6

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDS22-Sep-2015data reduction
XDS22-Sep-2015data scaling
REFMAC7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 1.6→46.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.572 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2091 2756 4.933 %
Rwork0.1852 --
all0.186 --
obs-55866 96.55 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.138 Å2
Baniso -1Baniso -2Baniso -3
1-0.679 Å20.339 Å20 Å2
2--0.679 Å20 Å2
3----2.203 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 110 197 2587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132601
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182188
X-RAY DIFFRACTIONr_angle_refined_deg0.961.6923560
X-RAY DIFFRACTIONr_angle_other_deg0.8771.6335118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9155323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49523.864132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03215363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.071158
X-RAY DIFFRACTIONr_chiral_restr0.0120.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.040.022928
X-RAY DIFFRACTIONr_gen_planes_other0.0340.02560
X-RAY DIFFRACTIONr_nbd_refined0.2150.2488
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21973
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21277
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1110.21100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2160
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3810.210
X-RAY DIFFRACTIONr_nbd_other0.1570.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1270.22
X-RAY DIFFRACTIONr_mcbond_it1.4151.7961229
X-RAY DIFFRACTIONr_mcbond_other1.4131.7961228
X-RAY DIFFRACTIONr_mcangle_it1.9282.6921551
X-RAY DIFFRACTIONr_mcangle_other1.9282.6921552
X-RAY DIFFRACTIONr_scbond_it2.0862.0051371
X-RAY DIFFRACTIONr_scbond_other2.0862.0051372
X-RAY DIFFRACTIONr_scangle_it3.1082.9372001
X-RAY DIFFRACTIONr_scangle_other3.1072.9372002
X-RAY DIFFRACTIONr_lrange_it4.12522.0393014
X-RAY DIFFRACTIONr_lrange_other4.02321.7782976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6410.3521440.3663163X-RAY DIFFRACTION78.3835
1.641-1.6860.341720.3343329X-RAY DIFFRACTION85.599
1.686-1.7350.3511720.2963488X-RAY DIFFRACTION91.9598
1.735-1.7880.2741900.2673597X-RAY DIFFRACTION96.7305
1.788-1.8470.2541990.2313530X-RAY DIFFRACTION99.7059
1.847-1.9120.251750.2123476X-RAY DIFFRACTION99.9726
1.912-1.9840.2011840.1843345X-RAY DIFFRACTION99.9151
1.984-2.0650.2041760.1773220X-RAY DIFFRACTION99.9706
2.065-2.1570.1851540.1573117X-RAY DIFFRACTION100
2.157-2.2620.1771690.1582956X-RAY DIFFRACTION99.936
2.262-2.3840.1891480.1532844X-RAY DIFFRACTION100
2.384-2.5290.1621490.1472675X-RAY DIFFRACTION100
2.529-2.7030.21420.1572532X-RAY DIFFRACTION100
2.703-2.920.1971180.1642375X-RAY DIFFRACTION100
2.92-3.1980.182990.1552211X-RAY DIFFRACTION100
3.198-3.5750.1731030.1632010X-RAY DIFFRACTION99.9527
3.575-4.1280.191740.1591785X-RAY DIFFRACTION99.9462
4.128-5.0530.157850.1541525X-RAY DIFFRACTION99.7522
5.053-7.1380.213640.2141211X-RAY DIFFRACTION99.3765
7.138-46.60.309390.211721X-RAY DIFFRACTION98.0645

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