[English] 日本語
Yorodumi
- PDB-2d6l: Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d6l
TitleCrystal structure of mouse galectin-9 N-terminal CRD (crystal form 2)
Componentslectin, galactose binding, soluble 9
KeywordsSUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein / galectin / Structural Genomics
Function / homology
Function and homology information


regulation of natural killer cell differentiation / positive regulation of oxidoreductase activity / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / galactoside binding / maintenance of protein location / positive regulation of interleukin-1 production / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of macrophage activation ...regulation of natural killer cell differentiation / positive regulation of oxidoreductase activity / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / galactoside binding / maintenance of protein location / positive regulation of interleukin-1 production / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of macrophage activation / positive regulation of innate immune response / heterophilic cell-cell adhesion / positive regulation of regulatory T cell differentiation / receptor clustering / negative regulation of type II interferon production / positive regulation of SMAD protein signal transduction / positive regulation of interleukin-10 production / immune system process / positive regulation of T cell migration / positive regulation of chemokine production / transforming growth factor beta receptor signaling pathway / positive regulation of cytokine production / protein serine/threonine kinase activator activity / female pregnancy / cellular response to virus / positive regulation of interleukin-6 production / negative regulation of inflammatory response / chemotaxis / positive regulation of tumor necrosis factor production / : / carbohydrate binding / response to lipopolysaccharide / signaling receptor binding / negative regulation of gene expression / enzyme binding / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNagae, M. / Nishi, N. / Nakamura, T. / Wakatsuki, S. / Kato, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition
Authors: Nagae, M. / Nishi, N. / Murata, T. / Usui, T. / Nakamura, T. / Wakatsuki, S. / Kato, R.
History
DepositionNov 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: lectin, galactose binding, soluble 9


Theoretical massNumber of molelcules
Total (without water)18,1701
Polymers18,1701
Non-polymers00
Water1,71195
1
X: lectin, galactose binding, soluble 9

X: lectin, galactose binding, soluble 9


Theoretical massNumber of molelcules
Total (without water)36,3402
Polymers36,3402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1/2,y+1/2,-z1
Unit cell
Length a, b, c (Å)56.406, 58.564, 48.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein lectin, galactose binding, soluble 9 / galectin-9


Mass: 18169.768 Da / Num. of mol.: 1
Fragment: N-terminal carbohydrate recognition domain(RESIDUES 1-157)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SXE6, UniProt: O08573*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% ethanol, 0.1M Tris (pH7.5) , VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 5937 / % possible obs: 99.8 % / Rmerge(I) obs: 0.107
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.315 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A3K

1a3k


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.318 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.929 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22916 268 4.5 %RANDOM
Rwork0.17779 ---
obs0.18015 5668 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 0 95 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9251725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22324.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12215216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.057155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021000
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2495
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2844
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.5777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05721235
X-RAY DIFFRACTIONr_scbond_it1.563556
X-RAY DIFFRACTIONr_scangle_it2.4914.5490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 14 -
Rwork0.194 429 -
obs--97.79 %

+
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