[English] 日本語
Yorodumi
- PDB-1ugw: Crystal structure of jacalin- Gal complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ugw
TitleCrystal structure of jacalin- Gal complex
Components
  • Agglutinin alpha chain
  • Agglutinin alpha-chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / All beta sheet protein / Beta prism I fold / Galactose specific
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (chempedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
Citation
Journal: J.MOL.BIOL. / Year: 2003
Title: Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study
Authors: Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes
Authors: Jeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: A Novel mode of carbohydrate recognition in jacalin, A moraceae plant lectin with a beta-prism fold
Authors: Sankaranarayanan, R. / Sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / Vijayan, M.
History
DepositionJun 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha-chain
D: Agglutinin beta-3 chain
E: Agglutinin alpha-chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,54312
Polymers66,8238
Non-polymers7214
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-66 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.444, 99.548, 105.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Agglutinin alpha chain / jacalin alpha chain


Mass: 14643.431 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / Organ: seeds / References: UniProt: P18670
#2: Protein/peptide
Agglutinin beta-3 chain / jacalin beta-3 chain


Mass: 2047.204 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / Organ: seeds / References: UniProt: P18673
#3: Protein Agglutinin alpha-chain / jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / Organ: seeds / References: UniProt: P18670
#4: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.94 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 4000, ammonium sulfate, sodium acetate trihydrate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.02 Mphosphate1droppH7.3
30.1 M1dropNaCl
40.025 %(w/v)sodium azide1drop
58-10 %PEG40001drop
640 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 91056 / Num. obs: 91056 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.447 / Num. unique all: 8911 / % possible all: 95.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. measured all: 350856
Reflection shell
*PLUS
% possible obs: 95.8 % / Num. unique obs: 8911

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M26

1m26


Resolution: 1.7→19.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2109195.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4565 5 %RANDOM
Rwork0.185 ---
obs0.185 91005 96.7 %-
all-91005 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9882 Å2 / ksol: 0.324271 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.3 Å20 Å20 Å2
2---4.17 Å20 Å2
3----3.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 48 489 5145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 747 5 %
Rwork0.287 14163 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CIS.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

+
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