[English] 日本語
Yorodumi
- PDB-6l68: X-ray structure of human galectin-10 in complex with D-allose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l68
TitleX-ray structure of human galectin-10 in complex with D-allose
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / beta-sandwich structure / lectin
Function / homology
Function and homology information


regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / : / carbohydrate binding / collagen-containing extracellular matrix / identical protein binding / cytosol
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
beta-D-allopyranose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKamitori, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals.
Authors: Itoh, A. / Nonaka, Y. / Nakakita, S.I. / Yoshida, H. / Nishi, N. / Nakamura, T. / Kamitori, S.
History
DepositionOct 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0043
Polymers16,6441
Non-polymers3602
Water1,08160
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0096
Polymers33,2882
Non-polymers7214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)48.900, 48.900, 259.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

-
Components

#1: Protein Galectin-10 / Gal-10 / Charcot-Leyden crystal protein / CLC / Eosinophil lysophospholipase / Lysolecithin acylhydrolase


Mass: 16644.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Escherichia coli (E. coli) / References: UniProt: Q05315
#2: Sugar ChemComp-ALL / beta-D-allopyranose / beta-D-allose / D-allose / allose / D-ALLOPYRANOSE


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-allopyranoseCOMMON NAMEGMML 1.0
b-D-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→19.61 Å / Num. obs: 14791 / % possible obs: 97.7 % / Redundancy: 19.9 % / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 1033 / CC1/2: 0.911

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QKQ

1qkq


Resolution: 1.92→19.607 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.643 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2093 747 5.05 %
Rwork0.1804 --
all0.182 --
obs-14791 97.714 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.015 Å20.007 Å20 Å2
2--0.015 Å20 Å2
3----0.048 Å2
Refinement stepCycle: LAST / Resolution: 1.92→19.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 24 60 1214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131182
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171068
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6731602
X-RAY DIFFRACTIONr_angle_other_deg1.2141.5942491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3195138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64322.90362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49515202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.763156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
X-RAY DIFFRACTIONr_nbd_refined0.1790.15157
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.15931
X-RAY DIFFRACTIONr_nbtor_refined0.1590.15541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.15539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.1548
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0720.153
X-RAY DIFFRACTIONr_nbd_other0.1730.1521
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.1516
X-RAY DIFFRACTIONr_mcbond_it1.2281.717555
X-RAY DIFFRACTIONr_mcbond_other1.221.713554
X-RAY DIFFRACTIONr_mcangle_it1.9242.557692
X-RAY DIFFRACTIONr_mcangle_other1.9232.561693
X-RAY DIFFRACTIONr_scbond_it2.0982.016627
X-RAY DIFFRACTIONr_scbond_other2.0982.016627
X-RAY DIFFRACTIONr_scangle_it3.422.911910
X-RAY DIFFRACTIONr_scangle_other3.4182.913911
X-RAY DIFFRACTIONr_lrange_it4.59219.3951193
X-RAY DIFFRACTIONr_lrange_other4.59919.3341189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.92-1.9690.219390.2149940.21410790.9210.92495.73680.164
1.969-2.0230.288580.2079510.21110480.8960.92996.27860.165
2.023-2.0810.198550.1928990.1929930.940.9496.07250.15
2.081-2.1440.227510.1829060.1849890.9340.9596.76440.146
2.144-2.2140.212510.1828970.1849780.9510.95296.93250.145
2.214-2.290.195400.178630.1719300.9580.95797.09680.137
2.29-2.3750.217450.1698220.1728890.9510.9697.52530.143
2.375-2.4710.234480.1728190.1758870.9440.96297.74520.145
2.471-2.5790.206370.1758000.1768520.9610.9698.23940.147
2.579-2.7020.205430.1857550.1868120.9560.9698.27590.155
2.702-2.8460.161330.1787270.1777720.9690.96798.44560.151
2.846-3.0140.209430.1866830.1877350.9530.95898.77550.16
3.014-3.2170.223310.1876610.1896980.9540.95899.14040.169
3.217-3.4670.255290.1696320.1736650.9390.96699.39850.157
3.467-3.7860.16420.175700.1696130.9730.96799.83690.16
3.786-4.2130.176220.1665420.1665650.9710.96999.8230.16
4.213-4.8280.18270.1434870.1455160.9730.97699.61240.145
4.828-5.8260.247200.1924210.1944410.9550.9641000.187
5.826-7.8970.288200.233590.2333790.9260.9461000.207
7.897-19.6070.219130.2272550.2272680.9540.9651000.236

+
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