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- PDB-2d6k: Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 2d6k
TitleCrystal structure of mouse galectin-9 N-terminal CRD (crystal form 1)
Componentslectin, galactose binding, soluble 9
KeywordsSUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein / galectin / Structural Genomics
Function / homology
Function and homology information


regulation of natural killer cell differentiation / positive regulation of oxidoreductase activity / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / galactoside binding / maintenance of protein location / positive regulation of interleukin-1 production / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of macrophage activation ...regulation of natural killer cell differentiation / positive regulation of oxidoreductase activity / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / galactoside binding / maintenance of protein location / positive regulation of interleukin-1 production / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of macrophage activation / positive regulation of innate immune response / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of regulatory T cell differentiation / receptor clustering / negative regulation of type II interferon production / positive regulation of interleukin-10 production / positive regulation of SMAD protein signal transduction / positive regulation of T cell migration / positive regulation of chemokine production / immune system process / transforming growth factor beta receptor signaling pathway / protein serine/threonine kinase activator activity / positive regulation of cytokine production / female pregnancy / cellular response to virus / positive regulation of interleukin-6 production / negative regulation of inflammatory response / chemotaxis / positive regulation of tumor necrosis factor production / : / carbohydrate binding / response to lipopolysaccharide / signaling receptor binding / negative regulation of gene expression / enzyme binding / extracellular region / nucleus / plasma membrane / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNagae, M. / Nishi, N. / Nakamura, T. / Murata, T. / Wakatsuki, S. / Kato, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition
Authors: Nagae, M. / Nishi, N. / Murata, T. / Usui, T. / Nakamura, T. / Wakatsuki, S. / Kato, R.
History
DepositionNov 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin, galactose binding, soluble 9
B: lectin, galactose binding, soluble 9


Theoretical massNumber of molelcules
Total (without water)36,3402
Polymers36,3402
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.094, 58.094, 221.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein lectin, galactose binding, soluble 9 / galectin-9


Mass: 18169.768 Da / Num. of mol.: 2
Fragment: N-terminal carbohydrate recognition domain(RESIDUES 1-157)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08573
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 15% ethanol, 0.1M CHES (pH9.5), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14051 / % possible obs: 99.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 35
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 7.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A3K

1a3k


Resolution: 2.5→35.25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.618 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28333 696 5 %RANDOM
Rwork0.20446 ---
obs0.20822 13283 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 0 99 2451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222419
X-RAY DIFFRACTIONr_bond_other_d0.0030.022
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9313268
X-RAY DIFFRACTIONr_angle_other_deg1.70933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8855287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91224.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86915402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9851511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021898
X-RAY DIFFRACTIONr_gen_planes_other00.021
X-RAY DIFFRACTIONr_nbd_refined0.2050.2965
X-RAY DIFFRACTIONr_nbd_other0.1420.21
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21599
X-RAY DIFFRACTIONr_nbtor_other0.1190.22
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.51477
X-RAY DIFFRACTIONr_mcbond_other0.0671.51
X-RAY DIFFRACTIONr_mcangle_it1.58722347
X-RAY DIFFRACTIONr_scbond_it2.12931047
X-RAY DIFFRACTIONr_scangle_it3.3464.5921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 48 -
Rwork0.266 943 -
obs--99.9 %

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