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- PDB-2iho: Crystal structure of MOA, a lectin from the mushroom Marasmius or... -

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Basic information

Entry
Database: PDB / ID: 2iho
TitleCrystal structure of MOA, a lectin from the mushroom Marasmius oreades in complex with the trisaccharide Gal(1,3)Gal(1,4)GlcNAc
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / beta-trefoil
Function / homology
Function and homology information


Beta Polymerase; domain 2 - #70 / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...Beta Polymerase; domain 2 - #70 / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Beta Polymerase; domain 2 / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMarasmius oreades (fairy-ring mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsGrahn, E. / Askarieh, G. / Holmner, A. / Tateno, H. / Winter, H.C. / Goldstein, I.J. / Krengel, U.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the marasmius oreades mushroom lectin in complex with a xenotransplantation epitope.
Authors: Grahn, E. / Askarieh, G. / Holmner, A. / Tateno, H. / Winter, H.C. / Goldstein, I.J. / Krengel, U.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4203
Polymers32,3291
Non-polymers1,0912
Water3,063170
1
A: Lectin
hetero molecules

A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8396
Polymers64,6572
Non-polymers2,1824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7250 Å2
ΔGint12 kcal/mol
Surface area22280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.640, 104.640, 112.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lectin / 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)
Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova blue DE3 / References: UniProt: Q8X123
#2: Polysaccharide beta-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 5.505585 Å3/Da / Density % sol: 77.65905 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Hepes, 2.4 M ammonium formate, 0.6 mg/ml N-ethylmaleimide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97905, 0.93952
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.939521
ReflectionResolution: 2.2→70 Å / Num. obs: 36670 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.11 / Net I/σ(I): 18
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 11 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5263 / Rsym value: 0.39 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.41→19.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.498 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.184 / ESU R Free: 0.161
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21126 1413 5 %RANDOM
Rwork0.19048 ---
obs0.19152 26661 99.59 %-
all-26661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.41→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 74 170 2521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212476
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9433394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6135307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0224.661118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77315352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.694157
X-RAY DIFFRACTIONr_chiral_restr0.1080.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021917
X-RAY DIFFRACTIONr_nbd_refined0.2090.21132
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.211
X-RAY DIFFRACTIONr_mcbond_it0.7921.51485
X-RAY DIFFRACTIONr_mcangle_it1.41822344
X-RAY DIFFRACTIONr_scbond_it2.38231161
X-RAY DIFFRACTIONr_scangle_it3.6394.51042
LS refinement shellResolution: 2.405→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 106 -
Rwork0.28 1911 -
obs--97.96 %

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