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- PDB-9ks7: Crystal structure of T. rubripes Mincle with glycerol -

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Basic information

Entry
Database: PDB / ID: 9ks7
TitleCrystal structure of T. rubripes Mincle with glycerol
ComponentsC-type lectin domain-containing protein
KeywordsIMMUNE SYSTEM / C-type lectin / ectodomain / Carbohydrate recognition doamin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
C-type lectin domain-containing protein
Similarity search - Component
Biological speciesTakifugu rubripes (torafugu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsIto, T. / Nagae, M. / Yamasaki, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Immunogenetics / Year: 2025
Title: Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates.
Authors: Ito, T. / Guenther, C. / Ishikawa, E. / Yabuki, T. / Nagae, M. / Nakatani, Y. / Yamasaki, S.
History
DepositionNov 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-type lectin domain-containing protein
B: C-type lectin domain-containing protein
E: C-type lectin domain-containing protein
G: C-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,33916
Polymers69,6504
Non-polymers68912
Water7,242402
1
A: C-type lectin domain-containing protein
E: C-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1698
Polymers34,8252
Non-polymers3456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-63 kcal/mol
Surface area13200 Å2
MethodPISA
2
B: C-type lectin domain-containing protein
G: C-type lectin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1698
Polymers34,8252
Non-polymers3456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-62 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.531, 72.371, 88.646
Angle α, β, γ (deg.)90.000, 94.431, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
C-type lectin domain-containing protein


Mass: 17412.408 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The sequence matches with Gene ID 105419054 (XP_029706534.1)
Source: (gene. exp.) Takifugu rubripes (torafugu) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B5KEF3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M tris (pH8.5), 0.2M sodium chloride, 25% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→45.99 Å / Num. obs: 71262 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.038 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3 / Num. unique obs: 3757 / CC1/2: 0.928 / Rpim(I) all: 0.227 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.19 Å / SU ML: 0.1531 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.5063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 3601 5.06 %
Rwork0.1734 67582 -
obs0.1745 71183 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.81 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 32 402 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864848
X-RAY DIFFRACTIONf_angle_d1.07266563
X-RAY DIFFRACTIONf_chiral_restr0.0701630
X-RAY DIFFRACTIONf_plane_restr0.0102847
X-RAY DIFFRACTIONf_dihedral_angle_d6.9415631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.25311510.24272582X-RAY DIFFRACTION99.13
1.72-1.750.2891390.23772556X-RAY DIFFRACTION99.93
1.75-1.770.2021600.21042629X-RAY DIFFRACTION99.86
1.77-1.80.2281310.19922559X-RAY DIFFRACTION99.93
1.8-1.830.23391530.18782593X-RAY DIFFRACTION99.96
1.83-1.860.19681330.18052611X-RAY DIFFRACTION99.75
1.86-1.890.20641530.17752580X-RAY DIFFRACTION99.74
1.89-1.920.22421220.18652585X-RAY DIFFRACTION99.71
1.92-1.960.19691280.17222597X-RAY DIFFRACTION99.78
1.96-20.19131300.1672625X-RAY DIFFRACTION99.86
2-2.040.19431390.16692574X-RAY DIFFRACTION99.85
2.04-2.090.22381380.17152581X-RAY DIFFRACTION99.96
2.09-2.140.20011500.16712632X-RAY DIFFRACTION99.89
2.14-2.20.21191570.15982577X-RAY DIFFRACTION99.82
2.2-2.260.21171400.16432589X-RAY DIFFRACTION99.56
2.26-2.340.20531570.16462600X-RAY DIFFRACTION99.71
2.34-2.420.18031250.17232593X-RAY DIFFRACTION99.67
2.42-2.520.21861310.17812604X-RAY DIFFRACTION99.71
2.52-2.630.21081300.18122590X-RAY DIFFRACTION99.67
2.63-2.770.21091250.17872640X-RAY DIFFRACTION99.57
2.77-2.940.21361300.17422604X-RAY DIFFRACTION99.45
2.95-3.170.22481500.18592605X-RAY DIFFRACTION99.49
3.17-3.490.16611520.17342571X-RAY DIFFRACTION99.13
3.49-40.17161310.15692621X-RAY DIFFRACTION98.99
4-5.030.15661250.14852607X-RAY DIFFRACTION98.24
5.04-44.190.19011210.18242677X-RAY DIFFRACTION98.35

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