[English] 日本語
Yorodumi
- PDB-2iho: Crystal structure of MOA, a lectin from the mushroom Marasmius or... -

+
Open data


ID or keywords:

Loading...

-
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 Marasmius)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 Marasmius)
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more