[English] 日本語
Yorodumi
- PDB-1g9f: CRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g9f
TitleCRYSTAL STRUCTURE OF THE SOYBEAN AGGLUTININ IN A COMPLEX WITH A BIANTENNARY BLOOD GROUP ANTIGEN ANALOG
ComponentsLECTIN
KeywordsSUGAR BINDING PROTEIN / JELLY-ROLL FOLD / LEGUME LECTIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsButs, L. / Hamelryck, T.W. / Dao-Thi, M.-H. / Loris, R. / Wyns, L. / Etzler, M.E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus.
Authors: Buts, L. / Dao-Thi, M.H. / Loris, R. / Wyns, L. / Etzler, M. / Hamelryck, T.
#1: Journal: Biochemistry / Year: 1997
Title: X-ray crystallographic studies of unique cross-linked lattices between four isomeric biantennary oligosaccharides and soybean agglutinin
Authors: Olsen, L.R. / Dessen, A. / Gupta, D. / Sabesan, S. / Sacchettini, J.C. / Brewer, C.F.
#2: Journal: Biochemistry / Year: 1995
Title: X-ray crystal structure of the soybean agglutinin cross-linked with a biantennary analog of the blood group I carbohydrate antigen
Authors: Dessen, A. / Gupta, D. / Sabesan, S. / Brewer, C.F. / Sacchettini, J.C.
History
DepositionNov 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0265
Polymers27,5961
Non-polymers1,4304
Water1629
1
A: LECTIN
hetero molecules

A: LECTIN
hetero molecules

A: LECTIN
hetero molecules

A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,10420
Polymers110,3834
Non-polymers5,72116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+1,x-1/2,z+1/41
crystal symmetry operation6_556x,-y+1/2,-z+5/41
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)122.640, 122.640, 90.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: - monomer B: symmetry -X,-Y,Z translation (245.28,0,0) - monomer C: symmetry -Y,-X,-Z translation (122.64,122.64,90,56) - monomer D: symmetry Y,X,-Z translation (122.64,122.64,90.56)

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein LECTIN / AGGLUTININ / SBA


Mass: 27595.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Organ: SEED / References: UniProt: P05046

-
Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2[DGalpb1-4DGlcpNAcb1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1/a2-b1_a3-d1_b4-c1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 11 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: protein,carbohydrate,HEPES,CaCl(2),MnCl(2),NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1reservoir
2100 mMsodium citrate1reservoir
38-12 %(w/v)PEG60001reservoir
40.2-0.4 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 72368 / Num. obs: 57894 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 2.9 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 3.7
Reflection
*PLUS
Num. all: 57894 / Num. obs: 19716 / % possible obs: 80 % / Num. measured all: 72368
Reflection shell
*PLUS
% possible obs: 72.7 %

-
Processing

Software
NameVersionClassification
X-PLORmodel building
CNS1refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: soybean agglutinin

Resolution: 2.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1969940.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1125 10.3 %RANDOM
Rwork0.19 ---
all0.19 10942 --
obs0.19 10942 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.72 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 92 9 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.261.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it3.822
X-RAY DIFFRACTIONc_scangle_it5.072.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 143 -
Rwork0.247 0 -
obs-1457 80.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / Rfactor Rwork: 0.247

+
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