[English] 日本語
Yorodumi
- PDB-5mwx: Galectin-1 in Complex with Ligand JB60 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mwx
TitleGalectin-1 in Complex with Ligand JB60
ComponentsGalectin-1
KeywordsTRANSFERASE / Sucrose Phosphorylase / bisp / Bifidobacterium
Function / homology
Function and homology information


galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding ...galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / cytosol / 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
BETA-MERCAPTOETHANOL / Chem-WYD / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.29 Å
AuthorsGrimm, C. / Bechold, J.
CitationJournal: To Be Published
Title: Galectin-1 in Complex with Ligand JB60
Authors: Grimm, C. / Bechold, J.
History
DepositionJan 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9876
Polymers29,5142
Non-polymers1,4744
Water3,441191
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-11 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.260, 58.250, 111.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Galectin-1 / / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14756.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-WYD / ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-4-[[1-[[3-(3-azanylprop-1-ynyl)phenyl]methyl]-1,2,3-triazol-4-yl]methoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-6-(hydroxymethyl)-4-oxidanyl-2-propoxy-oxan-3-yl]ethanamide


Mass: 649.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H43N5O11
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M AMMONIUM SULFATE, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.29→40.32 Å / Num. obs: 71546 / % possible obs: 99 % / Redundancy: 6.5 % / Net I/σ(I): 11.71

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXdev_2443refinement
PHASERdata processing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→40.319 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.55
RfactorNum. reflection% reflection
Rfree0.2049 3540 4.97 %
Rwork0.1688 --
obs0.1706 71171 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.25 Å2 / Biso mean: 28.8477 Å2 / Biso min: 11.2 Å2
Refinement stepCycle: final / Resolution: 1.29→40.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 105 191 2359
Biso mean--42.05 38.67 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0232353
X-RAY DIFFRACTIONf_angle_d1.6533204
X-RAY DIFFRACTIONf_chiral_restr0.116350
X-RAY DIFFRACTIONf_plane_restr0.011423
X-RAY DIFFRACTIONf_dihedral_angle_d22.87967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.29-1.30770.34131100.37432553266394
1.3077-1.32640.40451410.35872591273297
1.3264-1.34620.3611560.34312616277299
1.3462-1.36720.3581530.31712657281099
1.3672-1.38960.32811390.30322701284099
1.3896-1.41360.30441310.282626702801100
1.4136-1.43930.33891370.272626952832100
1.4393-1.4670.29081530.249326512804100
1.467-1.49690.27991360.237627122848100
1.4969-1.52950.22941240.197826952819100
1.5295-1.5650.22931600.16482654281499
1.565-1.60420.18961420.156727082850100
1.6042-1.64760.23241440.15726662810100
1.6476-1.6960.22261460.154727072853100
1.696-1.75080.18921350.160527042839100
1.7508-1.81340.19961170.147727542871100
1.8134-1.8860.19021240.138627382862100
1.886-1.97180.15281230.129827382861100
1.9718-2.07580.15481500.126527322882100
2.0758-2.20580.19251480.132927012849100
2.2058-2.37610.14591540.136327402894100
2.3761-2.61520.19831530.155127452898100
2.6152-2.99350.191500.164427662916100
2.9935-3.7710.19981440.160428052949100
3.771-40.33870.20631700.172829323102100

+
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