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- PDB-6tsp: Marasmius oreades agglutinin (MOA) inhibited by zinc -

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Basic information

Entry
Database: PDB / ID: 6tsp
TitleMarasmius oreades agglutinin (MOA) inhibited by zinc
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 mushroom)
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 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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)34,71019
Polymers32,3291
Non-polymers2,38218
Water2,468137
1
AAA: Agglutinin
hetero molecules

AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,42038
Polymers64,6572
Non-polymers4,76336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area11690 Å2
ΔGint-351 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.071, 121.071, 99.624
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-519-

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 mushroom)
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 , 6 types, 152 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 62.6 %
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, 0.5 M sodium acetate, 50 mM ZnCl2, 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: 1.28242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28242 Å / Relative weight: 1
ReflectionResolution: 1.85→46.4 Å / Num. obs: 64833 / % possible obs: 88.2 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 18.2
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 1.437 / Num. unique obs: 1507 / CC1/2: 0.489 / Rpim(I) all: 0.986 / Rrim(I) all: 1.767

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDSMar 15, 2019 BUILT=20190315data reduction
XDSMar 15, 2019 BUILT=20190315data scaling
PHASER7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 1.85→46.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.923 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2347 1872 5.242 %
Rwork0.2068 --
all0.208 --
obs-35709 94.566 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.884 Å2
Baniso -1Baniso -2Baniso -3
1-1.483 Å20.742 Å20 Å2
2--1.483 Å20 Å2
3----4.811 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 132 137 2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132559
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172184
X-RAY DIFFRACTIONr_angle_refined_deg0.8111.6893490
X-RAY DIFFRACTIONr_angle_other_deg0.5951.6285094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3775313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30523.84125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01415356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.43157
X-RAY DIFFRACTIONr_chiral_restr0.0110.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.022845
X-RAY DIFFRACTIONr_gen_planes_other0.0330.02548
X-RAY DIFFRACTIONr_nbd_refined0.2070.2477
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21964
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21252
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1050.21075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.1860.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.40.213
X-RAY DIFFRACTIONr_nbd_other0.2660.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1230.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2070.21
X-RAY DIFFRACTIONr_mcbond_it2.6753.3631207
X-RAY DIFFRACTIONr_mcbond_other2.6763.3631206
X-RAY DIFFRACTIONr_mcangle_it3.1065.0451517
X-RAY DIFFRACTIONr_mcangle_other3.1065.0451518
X-RAY DIFFRACTIONr_scbond_it3.3883.6741352
X-RAY DIFFRACTIONr_scbond_other3.3873.6741353
X-RAY DIFFRACTIONr_scangle_it4.4795.3971967
X-RAY DIFFRACTIONr_scangle_other4.4775.3971968
X-RAY DIFFRACTIONr_lrange_it5.19939.7692915
X-RAY DIFFRACTIONr_lrange_other5.19239.6852900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8890.511020.4371748X-RAY DIFFRACTION67.5923
1.889-1.9410.3691130.3781978X-RAY DIFFRACTION78.6386
1.941-1.9970.3831320.3172102X-RAY DIFFRACTION85.89
1.997-2.0590.3171220.2742227X-RAY DIFFRACTION92.8458
2.059-2.1260.281000.2542342X-RAY DIFFRACTION99.3895
2.126-2.2010.3131190.2612253X-RAY DIFFRACTION99.8737
2.201-2.2840.2551110.212194X-RAY DIFFRACTION100
2.284-2.3770.2691260.2282095X-RAY DIFFRACTION100
2.377-2.4830.2481250.2051996X-RAY DIFFRACTION100
2.483-2.6040.2221010.1721926X-RAY DIFFRACTION99.7539
2.604-2.7450.2151070.1611842X-RAY DIFFRACTION99.8975
2.745-2.9110.222980.1731749X-RAY DIFFRACTION99.9459
2.911-3.1120.2980.1781649X-RAY DIFFRACTION99.8857
3.112-3.3610.208800.1921547X-RAY DIFFRACTION99.9386
3.361-3.6810.207730.1971437X-RAY DIFFRACTION100
3.681-4.1150.2750.1861294X-RAY DIFFRACTION99.7813
4.115-4.750.16690.1441169X-RAY DIFFRACTION99.9193
4.75-5.8150.209510.1991006X-RAY DIFFRACTION99.8111
5.815-8.2110.266470.256791X-RAY DIFFRACTION100
8.211-46.40.319230.238493X-RAY DIFFRACTION98.4733

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