[English] 日本語
Yorodumi
- PDB-1pxd: Crystal structure of the complex of jacalin with meso-tetrasulpho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pxd
TitleCrystal structure of the complex of jacalin with meso-tetrasulphonatophenylporphyrin.
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / lectin / porphyrin
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-SFP / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoel, M. / Anuradha, P. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction.
Authors: Goel, M. / Anuradha, P. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Functional equality in the absence of structural similarity: an added dimension to molecular mimicry
Authors: Goel, M. / Jain, D. / Kaur, K.J. / Kenoth, R. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
History
DepositionJul 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6114
Polymers16,7332
Non-polymers1,8782
Water1,02757
1
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,44316
Polymers66,9318
Non-polymers7,5128
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area17980 Å2
ΔGint-85 kcal/mol
Surface area27440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.072, 101.890, 107.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Agglutinin alpha chain / Jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18670
#2: Protein/peptide Agglutinin beta-3 chain / Jacalin beta-3 chain


Mass: 2059.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / References: UniProt: P18673
#3: Chemical ChemComp-SFP / 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE


Mass: 939.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H34N4O12S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.8 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Ammonium sulphate and Sodium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 2002
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 23948 / Num. obs: 23948 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 10.8 / Num. unique all: 23948 / % possible all: 79.9

-
Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAC

1jac


Resolution: 1.8→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1916 -RANDOM
Rwork0.219 ---
all0.219 19451 --
obs0.219 19451 81.2 %-
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 128 57 1338

+
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://pdbjlvh1.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