[English] 日本語
Yorodumi
- PDB-4wvw: Chicken Galectin-8 N-terminal domain complexed with 3'-sialyl-lactose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wvw
TitleChicken Galectin-8 N-terminal domain complexed with 3'-sialyl-lactose
ComponentsGalectin
KeywordsSUGAR BINDING PROTEIN / Lectin / carbohydrate recognition domain
Function / homology
Function and homology information


carbohydrate binding
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
3'-sialyl-alpha-lactose / DI(HYDROXYETHYL)ETHER / Galectin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsRuiz, F.M. / Romero, A.
CitationJournal: Chemistry / Year: 2015
Title: Combining Crystallography and Hydrogen-Deuterium Exchange to Study Galectin-Ligand Complexes.
Authors: Ruiz, F.M. / Gilles, U. / Lindner, I. / Andre, S. / Romero, A. / Reusch, D. / Gabius, H.J.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2643
Polymers16,5241
Non-polymers7402
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint7 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.459, 56.459, 198.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-373-

HOH

-
Components

#1: Protein Galectin / / Galectin 8


Mass: 16524.283 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 9-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pqe60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1W2P6
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 30% w/v PEG 4000, 100 Mm Tris-HCl pH 8.5, 200 mM Sodium Acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.47→49.75 Å / Num. all: 33211 / Num. obs: 33211 / % possible obs: 100 % / Redundancy: 16.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.1
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.807 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 23984 / Num. unique all: 1610 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YV8

2yv8


Resolution: 1.47→47.48 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 3098 5.13 %
Rwork0.1764 57300 -
obs0.1773 60398 100 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.05 Å2 / Biso mean: 21.5999 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: final / Resolution: 1.47→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 50 191 1405
Biso mean--23.36 33.97 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071278
X-RAY DIFFRACTIONf_angle_d1.6281739
X-RAY DIFFRACTIONf_chiral_restr0.089200
X-RAY DIFFRACTIONf_plane_restr0.006213
X-RAY DIFFRACTIONf_dihedral_angle_d12.859475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.47-1.4930.35131200.291626322752
1.493-1.51750.2821510.262225872738
1.5175-1.54360.30921200.273126182738
1.5436-1.57170.2451410.235926292770
1.5717-1.60190.22771690.215125802749
1.6019-1.63460.23211380.21225742712
1.6346-1.67020.20961500.193626142764
1.6702-1.7090.19611170.193726552772
1.709-1.75180.19351360.191525712707
1.7518-1.79910.21841610.183925982759
1.7991-1.85210.22041610.176925652726
1.8521-1.91190.18171650.166125812746
1.9119-1.98020.18341380.164825932731
1.9802-2.05950.20411600.163625842744
2.0595-2.15320.21271220.157326342756
2.1532-2.26670.17071410.157926192760
2.2667-2.40870.21321190.170626232742
2.4087-2.59470.23641360.181826072743
2.5947-2.85580.21321540.183325852739
2.8558-3.2690.17451250.175926322757
3.269-4.11820.16441570.142225752732
4.1182-47.50740.13811170.16926442761
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)
10.3934-0.4640.48861.2617-0.08830.9362-0.0335-0.05530.0312-0.125-0.07170.3401-0.1972-0.48270.06470.1970.07270.00650.1715-0.05530.1815-7.842215.40930.3558
21.7415-0.06540.77382.23450.51140.8689-0.00930.06010.1666-0.16480.0743-0.0374-0.36650.17-0.11860.1749-0.03280.02630.072-0.03510.12616.442720.3378-1.1244
30.9018-0.6653-0.24423.38563.06343.66920.108-0.35620.2450.33920.0871-0.3153-0.24270.2468-0.10280.2188-0.06850.0220.165-0.09270.187713.732819.34397.9898
41.0077-0.39250.37131.76470.49311.99560.0610.0090.0004-0.061-0.02160.0176-0.0361-0.0407-0.03690.0977-0.00920.01820.0611-0.02970.09361.840310.6916-1.4661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 9:37)A9 - 37
2X-RAY DIFFRACTION2(chain A and resid 38:80)A38 - 80
3X-RAY DIFFRACTION3(chain A and resid 81:90)A81 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:152)A91 - 152

+
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