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- PDB-2gal: CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSE -

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Basic information

Entry
Database: PDB / ID: 2gal
TitleCRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSE
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
beta-D-galactopyranose / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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 1.4Feb 14, 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,2924
Polymers29,9322
Non-polymers3602
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.470, 64.520, 72.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.364826, -0.736594, 0.569501), (-0.776798, -0.096414, -0.622325), (0.513309, -0.669428, -0.53701)
Vector: 47.25281, 59.21492, 28.66626)

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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-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %
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 GALACTOSE. 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 GALACTOSE., 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

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 18155 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.384 / % possible all: 97.4
Reflection
*PLUS
Num. measured all: 172647
Reflection shell
*PLUS
% possible obs: 97.4 %

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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: 2→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
Rfree0.245 847 4.8 %RANDOM
Rwork0.187 ---
obs0.187 17475 98.4 %-
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 12 76 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.081.5
X-RAY DIFFRACTIONx_mcangle_it3.32
X-RAY DIFFRACTIONx_scbond_it3.712
X-RAY DIFFRACTIONx_scangle_it5.752.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 141 5 %
Rwork0.243 2686 -
obs--97.8 %
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
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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