[English] 日本語
Yorodumi
- PDB-3gal: CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gal
TitleCRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE
ComponentsGALECTIN-7
KeywordsLECTIN / GALAPTIN / GALECTIN / CARBOHYDRATE BINDING
Function / homology
Function and homology information


Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / 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
2-amino-2-deoxy-beta-D-galactopyranose / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeonidas, D.D. / Acharya, K.R.
CitationJournal: Biochemistry / Year: 1998
Title: Structural basis for the recognition of carbohydrates by human galectin-7.
Authors: Leonidas, D.D. / Vatzaki, E.H. / Vorum, H. / Celis, J.E. / Madsen, P. / Acharya, K.R.
History
DepositionJul 13, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GALECTIN-7
B: GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2904
Polymers29,9322
Non-polymers3582
Water1,56787
1
A: GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1452
Polymers14,9661
Non-polymers1791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GALECTIN-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1452
Polymers14,9661
Non-polymers1791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.590, 54.620, 61.200
Angle α, β, γ (deg.)90.00, 115.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1026-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997677, -0.066346, -0.01544), (-0.009592, 0.36123, -0.932427), (0.06744, -0.930113, -0.361028)
Vector: -12.19768, 6.97048, 11.58594)

-
Components

#1: Protein GALECTIN-7


Mass: 14965.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P47929
#2: Sugar ChemComp-1GN / 2-amino-2-deoxy-beta-D-galactopyranose / beta-D-galactosamine / 2-amino-2-deoxy-beta-D-galactose / 2-amino-2-deoxy-D-galactose / 2-amino-2-deoxy-galactose / 2-DEOXY-2-AMINOGALACTOSE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGalpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.4 Å3/Da / Density % sol: 48.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.1
Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND ...Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND 25 MM GALACTOSAMINE. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350 AND 50 MM GALACTOSAMINE., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
250 mMsodium phosphate1drop
30.3 M1dropNaCl
420 mMimidazol1drop
58.5 %PEG33501drop
650 mMsodium phosphate1reservoir
70.3 M1reservoirNaCl
820 mMimidazole1reservoir
917 %PEG33501reservoir

-
Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 22372 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.363 / % possible all: 98
Reflection
*PLUS
Num. measured all: 132648
Reflection shell
*PLUS
% possible obs: 98 %

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FREE GALECTIN-7

Resolution: 1.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1085 4.9 %RANDOM
Rwork0.211 ---
obs0.211 22335 98.6 %-
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 24 87 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.941.5
X-RAY DIFFRACTIONx_mcangle_it3.252
X-RAY DIFFRACTIONx_scbond_it3.162
X-RAY DIFFRACTIONx_scangle_it4.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 184 5 %
Rwork0.299 3488 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REPTOPHCSDX.PR
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8

+
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