[English] 日本語
Yorodumi
- PDB-2uvo: High Resolution Crystal Structure of Wheat Germ Agglutinin in Com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uvo
TitleHigh Resolution Crystal Structure of Wheat Germ Agglutinin in Complex with N-Acetyl-D-Glucosamine
ComponentsAGGLUTININ ISOLECTIN 1
KeywordsCARBOHYDRATE-BINDING PROTEIN / HEVEIN DOMAIN / CHITIN-BINDING / WHEAT GERM AGGLUTININ / CHITIN-BINDING PROTEIN / N-ACETYL-D- GLUCOSAMINE / WGA / GLCNAC / CHITIN / LECTIN / ANTIFUNGAL / PROTEIN-CARBOHYDRATE INTERACTION
Function / homology
Function and homology information


chitin binding / carbohydrate binding
Similarity search - Function
Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / Agglutinin isolectin 1
Similarity search - Component
Biological speciesTRITICUM AESTIVUM (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchwefel, D. / Wittmann, V. / Diederichs, K. / Welte, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Structural Basis of Multivalent Binding to Wheat Germ Agglutinin.
Authors: Schwefel, D. / Maierhofer, C. / Beck, J.G. / Seeberger, S. / Diederichs, K. / Moller, H.M. / Welte, W. / Wittmann, V.
History
DepositionMar 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_symm_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_symm_contact.auth_atom_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AGGLUTININ ISOLECTIN 1
B: AGGLUTININ ISOLECTIN 1
E: AGGLUTININ ISOLECTIN 1
F: AGGLUTININ ISOLECTIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84626
Polymers68,4964
Non-polymers4,35022
Water11,223623
1
A: AGGLUTININ ISOLECTIN 1
B: AGGLUTININ ISOLECTIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,64414
Polymers34,2482
Non-polymers2,39612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-36 kcal/mol
Surface area17940 Å2
MethodPQS
2
E: AGGLUTININ ISOLECTIN 1
F: AGGLUTININ ISOLECTIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,20212
Polymers34,2482
Non-polymers1,95410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-41.1 kcal/mol
Surface area18040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.390, 91.510, 94.500
Angle α, β, γ (deg.)90.00, 82.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
AGGLUTININ ISOLECTIN 1 / WGA1 / ISOLECTIN A / WHEAT GERM AGGLUTININ


Mass: 17124.080 Da / Num. of mol.: 4 / Fragment: RESIDUES 27-197 / Source method: isolated from a natural source / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P10968
#2: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: CRYSTALLIZATION BUFFER: 20 MM SODIUM ACETATE, 6 MM CACL2, 4 % ETHANOL RESERVOIR: 0.04 M POTASSIUM DIHYDROGEN PHOSPHATE, 16 % PEG 8000, 20 % GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→37.48 Å / Num. obs: 137253 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.87
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.27 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
REFMAC5.3.0022refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WGT

1wgt


Resolution: 1.4→93.66 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.223 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOLLOWING RESIDUES WERE MODELED IN ATERNATIVE CONFORMATIONS LYS A 33, LYS A 134, SER A 152, MET B 26, MET E 10, LEU E 16, LYS E 33, ALA E ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOLLOWING RESIDUES WERE MODELED IN ATERNATIVE CONFORMATIONS LYS A 33, LYS A 134, SER A 152, MET B 26, MET E 10, LEU E 16, LYS E 33, ALA E 53, MET F 10, MET F 26, SER F 91, ARG F 139. FOLLOWING RESIDUES WERE MODELED WITH OCCUPANCY LOWER THAN 1 BECAUSE OF RADIATION DAMAGE OR MISSING DENSITY DUE TO FLEXIBILITY GLU A 5, GLU B 5, GLU E 5, GLY E 171, GLU F 5, ASP F 135, GLY F 171.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6879 5 %RANDOM
Rwork0.181 ---
obs0.182 130373 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.12 Å2
2--0.41 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→93.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 294 623 5580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215190
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.17527012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4085707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0625.337193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00115704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7831517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023977
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.22496
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23612
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.53397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26125121
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34432051
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6544.51878
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 511
Rwork0.278 9907

+
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