[English] 日本語
Yorodumi
- PDB-6wab: Crystal structure of human galectin-4 C-terminal carbohydrate rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wab
TitleCrystal structure of human galectin-4 C-terminal carbohydrate recognition domain in complex with galactose derivative
ComponentsGalectin-4
KeywordsSUGAR BINDING PROTEIN / GALECTIN / LECTIN / BETA SANDWICH / CARBOHYDRATE RECOGNITION / CARBOHYDRATE BINDING PROTEIN
Function / homology
Function and homology information


antibacterial peptide biosynthetic process / galactoside binding / : / carbohydrate binding / cell adhesion / extracellular space / plasma membrane / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-U61 / Galectin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsGo, R.M. / Kishor, C. / Blanchard, H.
CitationJournal: To Be Published
Title: Crystal structure of human galectin-4 C-terminal carbohydrate recognition domain in complex with galactose derivative
Authors: Go, R.M. / Kishor, C. / Blanchard, H.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin-4
B: Galectin-4
C: Galectin-4
D: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8798
Polymers61,7624
Non-polymers1,1174
Water1,67593
1
A: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0914
Polymers15,4411
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9072
Polymers15,4411
Non-polymers4661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galectin-4


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galectin-4


Theoretical massNumber of molelcules
Total (without water)15,4411
Polymers15,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.698, 128.558, 45.891
Angle α, β, γ (deg.)90.000, 101.219, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Galectin-4 / Gal-4 / Antigen NY-CO-27 / L-36 lactose-binding protein / L36LBP / Lactose-binding lectin 4


Mass: 15440.567 Da / Num. of mol.: 4 / Fragment: C-terminal carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS4 / Production host: Escherichia coli (E. coli) / References: UniProt: P56470
#2: Chemical ChemComp-U61 / 2,6-anhydro-1,4-dideoxy-1-[4-(4-fluorophenyl)-1H-1,2,3-triazol-1-yl]-4-(4-phenyl-1H-1,2,3-triazol-1-yl)-D-glycero-L-manno-heptitol


Mass: 466.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23FN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6 M ammonium sulfate, 4% (v/v) polyethylene glycol (PEG) 400, 0.1 M HEPES pH 7.0
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.28→45.01 Å / Num. obs: 23306 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.992 / Net I/σ(I): 6.8
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 2251 / CC1/2: 0.766

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YM2

4ym2


Resolution: 2.28→36.795 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.744 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.49 / ESU R Free: 0.281
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2662 1214 5.219 %
Rwork0.1967 --
all0.2 --
obs-23261 98.343 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.074 Å2
Baniso -1Baniso -2Baniso -3
1-0.023 Å20 Å2-0.003 Å2
2---0.025 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 2.28→36.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 80 93 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134552
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174182
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6776172
X-RAY DIFFRACTIONr_angle_other_deg1.2081.5929678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4665552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.32820.694245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93615703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.851537
X-RAY DIFFRACTIONr_chiral_restr0.0650.2574
X-RAY DIFFRACTIONr_chiral_restr_other1.5270.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021061
X-RAY DIFFRACTIONr_nbd_refined0.1980.2702
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23875
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22076
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.22275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2165
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.231
X-RAY DIFFRACTIONr_nbd_other0.2050.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.215
X-RAY DIFFRACTIONr_mcbond_it3.0973.7222208
X-RAY DIFFRACTIONr_mcbond_other3.0973.7222207
X-RAY DIFFRACTIONr_mcangle_it4.4455.5692754
X-RAY DIFFRACTIONr_mcangle_other4.4455.572755
X-RAY DIFFRACTIONr_scbond_it3.3453.9812344
X-RAY DIFFRACTIONr_scbond_other3.3453.9822344
X-RAY DIFFRACTIONr_scangle_it4.9035.8463416
X-RAY DIFFRACTIONr_scangle_other4.9025.8463416
X-RAY DIFFRACTIONr_lrange_it6.97742.1034644
X-RAY DIFFRACTIONr_lrange_other6.97942.1064640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3390.313930.2111593X-RAY DIFFRACTION98.2517
2.339-2.4030.306840.2391613X-RAY DIFFRACTION98.2629
2.403-2.4730.322710.2191530X-RAY DIFFRACTION98.5231
2.473-2.5490.359830.2291520X-RAY DIFFRACTION98.0428
2.549-2.6320.297990.1991424X-RAY DIFFRACTION99.3477
2.632-2.7240.299870.2081399X-RAY DIFFRACTION97.9565
2.724-2.8270.242810.1951359X-RAY DIFFRACTION99.1053
2.827-2.9420.297680.191307X-RAY DIFFRACTION98.7078
2.942-3.0730.264550.1851288X-RAY DIFFRACTION98.3883
3.073-3.2220.285670.1821186X-RAY DIFFRACTION99.1297
3.222-3.3960.228470.1811150X-RAY DIFFRACTION98.681
3.396-3.6020.292800.1871054X-RAY DIFFRACTION97.6744
3.602-3.8490.204420.1921012X-RAY DIFFRACTION96.5201
3.849-4.1570.245570.184968X-RAY DIFFRACTION98.7476
4.157-4.5510.198440.17869X-RAY DIFFRACTION99.3471
4.551-5.0860.286510.182785X-RAY DIFFRACTION98.7013
5.086-5.8660.282310.205706X-RAY DIFFRACTION98.5294
5.866-7.170.261400.21573X-RAY DIFFRACTION97.9233
7.17-10.0770.216190.213460X-RAY DIFFRACTION97.1602

+
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