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- PDB-2d6l: Crystal structure of mouse galectin-9 N-terminal CRD (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 2d6l
TitleCrystal structure of mouse galectin-9 N-terminal CRD (crystal form 2)
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 / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / positive regulation of oxidoreductase activity / 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 / negative regulation of natural killer cell degranulation / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / positive regulation of oxidoreductase activity / 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 / immune system process / positive regulation of T cell migration / positive regulation of chemokine production / 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. / 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:
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Assembly

Deposited unit
X: lectin, galactose binding, soluble 9


Theoretical massNumber of molelcules
Total (without water)18,1701
Polymers18,1701
Non-polymers00
Water1,71195
1
X: lectin, galactose binding, soluble 9

X: lectin, galactose binding, soluble 9


Theoretical massNumber of molelcules
Total (without water)36,3402
Polymers36,3402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1/2,y+1/2,-z1
Unit cell
Length a, b, c (Å)56.406, 58.564, 48.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 18169.768 Da / Num. of mol.: 1
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: Q5SXE6, UniProt: O08573*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 44.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% ethanol, 0.1M Tris (pH7.5) , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / 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: 5937 / % possible obs: 99.8 % / Rmerge(I) obs: 0.107
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.315 / % possible all: 98.2

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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→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 7.318 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.929 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22916 268 4.5 %RANDOM
Rwork0.17779 ---
obs0.18015 5668 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 0 95 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9251725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22324.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12215216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.057155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021000
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2495
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2844
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.5777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05721235
X-RAY DIFFRACTIONr_scbond_it1.563556
X-RAY DIFFRACTIONr_scangle_it2.4914.5490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 14 -
Rwork0.194 429 -
obs--97.79 %

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