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

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Basic information

Entry
Database: PDB / ID: 6tsm
TitleMarasmius oreades agglutinin (MOA) in complex with the truncated PVVRAHS synthetic substrate
Components
  • Agglutinin
  • PRO-VAL-VAL-ARG
KeywordsSUGAR BINDING PROTEIN / 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: 1.4 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
BBB: PRO-VAL-VAL-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8659
Polymers32,7002
Non-polymers1,1657
Water4,522251
1
AAA: Agglutinin
BBB: PRO-VAL-VAL-ARG
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)67,73018
Polymers65,4004
Non-polymers2,33014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area9060 Å2
ΔGint-46 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.155, 122.155, 100.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AAABBB

#1: Protein Agglutinin


Mass: 32229.578 Da / Num. of mol.: 1 / Mutation: C215A, 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-VAL-ARG


Mass: 470.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetic proteolysis substrate / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Sugars , 2 types, 2 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-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, 256 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 crystal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylate/HCl pH 6.5, 20% PEG 8000, 0.2 M sodium acetate, 10 mM CaCl2, 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: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.4→46.8 Å / Num. obs: 87357 / % possible obs: 99.8 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.035 / Rrim(I) all: 0.152 / Net I/σ(I): 11.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 17.8 % / Rmerge(I) obs: 5.335 / Mean I/σ(I) obs: 0.362 / Num. unique obs: 4152 / CC1/2: 0.362 / Rpim(I) all: 1.266 / Rrim(I) all: 5.489 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDS29-Nov-2019data reduction
XDS29-Nov-2019data scaling
REFMAC7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 1.4→46.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.296 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1978 4388 5.025 %
Rwork0.179 --
all0.18 --
obs-87323 99.8 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.547 Å20.274 Å20 Å2
2--0.547 Å20 Å2
3----1.775 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 74 251 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132605
X-RAY DIFFRACTIONr_bond_other_d0.0040.0182267
X-RAY DIFFRACTIONr_angle_refined_deg0.8761.6783579
X-RAY DIFFRACTIONr_angle_other_deg0.6051.6145304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2295338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25323.282131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0281510
X-RAY DIFFRACTIONr_chiral_restr0.0160.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0420.022958
X-RAY DIFFRACTIONr_gen_planes_other0.0350.02572
X-RAY DIFFRACTIONr_nbd_refined0.2180.2433
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21993
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21259
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1010.21117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2520.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1560.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3150.212
X-RAY DIFFRACTIONr_nbd_other0.1740.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1460.22
X-RAY DIFFRACTIONr_mcbond_it1.4972.0491237
X-RAY DIFFRACTIONr_mcbond_other1.4822.0481236
X-RAY DIFFRACTIONr_mcangle_it2.1773.071557
X-RAY DIFFRACTIONr_mcangle_other2.1773.0711558
X-RAY DIFFRACTIONr_scbond_it2.2372.2711367
X-RAY DIFFRACTIONr_scbond_other2.2292.2721367
X-RAY DIFFRACTIONr_scangle_it3.3773.3212001
X-RAY DIFFRACTIONr_scangle_other3.3773.3232001
X-RAY DIFFRACTIONr_lrange_it4.38124.4422973
X-RAY DIFFRACTIONr_lrange_other4.3824.4462974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4310.3543070.3535919X-RAY DIFFRACTION98.0009
1.431-1.470.2973110.3245914X-RAY DIFFRACTION99.9037
1.47-1.5120.2882910.2995752X-RAY DIFFRACTION99.9504
1.512-1.5590.2912940.2745576X-RAY DIFFRACTION99.9659
1.559-1.610.2652860.255440X-RAY DIFFRACTION100
1.61-1.6670.252940.2225222X-RAY DIFFRACTION99.9819
1.667-1.7290.2262620.1945075X-RAY DIFFRACTION100
1.729-1.80.1912750.1724891X-RAY DIFFRACTION100
1.8-1.880.1862640.1654674X-RAY DIFFRACTION99.9798
1.88-1.9720.1882370.1674494X-RAY DIFFRACTION100
1.972-2.0780.1942040.1694306X-RAY DIFFRACTION100
2.078-2.2040.1862260.1634040X-RAY DIFFRACTION99.9766
2.204-2.3570.1912060.1563839X-RAY DIFFRACTION100
2.357-2.5450.1871830.1623597X-RAY DIFFRACTION100
2.545-2.7880.1881980.1723284X-RAY DIFFRACTION100
2.788-3.1170.2041600.1743003X-RAY DIFFRACTION100
3.117-3.5980.1781330.172699X-RAY DIFFRACTION100
3.598-4.4060.1641140.1452297X-RAY DIFFRACTION100
4.406-6.2260.156910.1531818X-RAY DIFFRACTION99.8953
6.226-46.80.221520.1831095X-RAY DIFFRACTION99.4796

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