[English] 日本語
Yorodumi
- PDB-3t2t: Crystal structure of human galectin-1 in complex with methyl 2-O-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t2t
TitleCrystal structure of human galectin-1 in complex with methyl 2-O-acetyl-3-O-toluoyl-beta-D-talopyranoside
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN/INHIBITOR / beta sandwich / lectin / SUGAR BINDING PROTEIN-INHIBITOR complex
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 / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / 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
Chem-MQT / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsBlanchard, H. / Collins, P.M.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Taloside inhibitors of galectin-1 and galectin-3
Authors: Collins, P.M. / Oberg, C.T. / Leffler, H. / Nilsson, U.J. / Blanchard, H.
History
DepositionJul 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / struct_conn ...chem_comp / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
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)30,2723
Polymers29,9182
Non-polymers3541
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.687, 58.444, 112.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 134
2114B1 - 134

-
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: 14959.027 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: Sugar ChemComp-MQT / methyl 2-O-acetyl-3-O-(4-methylbenzoyl)-beta-D-talopyranoside / methyl 2-O-acetyl-3-O-4-toluoyl-beta-D-talopyranoside / Methyl group


Type: D-saccharide / Mass: 354.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2M ammonium sulphate, 25% w/v polyethylene glycol 4000, 0.1M sodium acetate trihydrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 16, 2009
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→112 Å / Num. all: 22727 / Num. obs: 21603 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.949 Å / % possible all: 91.7

-
Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
AMoREphasing
REFMAC5.5.0109refinement
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→56.14 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.034 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22623 1154 5.1 %RANDOM
Rwork0.18764 ---
all0.2 22727 --
obs0.18963 21603 94.94 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 26.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---1.51 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→56.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 25 134 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222182
X-RAY DIFFRACTIONr_bond_other_d0.0010.021477
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.982956
X-RAY DIFFRACTIONr_angle_other_deg0.7733616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4875278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96525.283106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09315338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2511510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.94441350
X-RAY DIFFRACTIONr_mcbond_other1.4984548
X-RAY DIFFRACTIONr_mcangle_it5.62862162
X-RAY DIFFRACTIONr_scbond_it4.2543832
X-RAY DIFFRACTIONr_scangle_it6.3334.5788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1681 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.390.5
medium thermal1.012
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 76 -
Rwork0.271 1506 -
obs--89.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9064-0.0442-0.26472.3655-0.17992.24740.1188-0.00410.0602-0.0440.025-0.01760.1929-0.0739-0.14370.0417-0.0089-0.02090.06610.00950.034412.0327.59812.964
21.4536-0.10590.46673.543-0.08251.8845-0.1094-0.00580.01740.058-0.01140.2478-0.0757-0.07850.12080.00050.0049-0.00160.06960.00080.039110.87336.46911.494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 134
2X-RAY DIFFRACTION2B1 - 134

+
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