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- PDB-6kzr: Crystal structure of mouse DCAR2 CRD domain -

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Basic information

Entry
Database: PDB / ID: 6kzr
TitleCrystal structure of mouse DCAR2 CRD domain
ComponentsC-type lectin domain family 4, member b1
KeywordsSUGAR BINDING PROTEIN / C-type lectin
Function / homology
Function and homology information


antifungal innate immune response / positive regulation of release of sequestered calcium ion into cytosol / signaling receptor activity / carbohydrate binding / external side of plasma membrane / metal ion binding
Similarity search - Function
CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 ...CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
C-type lectin domain family 4, member b1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsOmahdi, Z. / Horikawa, Y. / Toyonaga, K. / Teramoto, T. / Kakuta, Y. / Yamasaki, S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR.
Authors: Omahdi, Z. / Horikawa, Y. / Nagae, M. / Toyonaga, K. / Imamura, A. / Takato, K. / Teramoto, T. / Ishida, H. / Kakuta, Y. / Yamasaki, S.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-type lectin domain family 4, member b1
B: C-type lectin domain family 4, member b1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1628
Polymers31,7142
Non-polymers4496
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-22 kcal/mol
Surface area13480 Å2
2
A: C-type lectin domain family 4, member b1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0814
Polymers15,8571
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-9 kcal/mol
Surface area7350 Å2
MethodPISA
3
B: C-type lectin domain family 4, member b1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0814
Polymers15,8571
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-9 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.979, 72.435, 101.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C-type lectin domain family 4, member b1 / Dendritic cell immuno-activating receptor beta isoform


Mass: 15856.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clec4b1, Clec4b, Dcar / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D8Q7
#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.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4 Å3/Da / Density % sol: 69.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→58.9 Å / Num. obs: 22002 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 3468 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LFJ

6lfj


Resolution: 2.304→43.971 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.162 / Average fsc free: 0.9218 / Average fsc work: 0.9354 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2207 1141 5.186 %
Rwork0.1888 20861 -
all0.19 --
obs-22002 99.724 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.237 Å20 Å20 Å2
2---0.178 Å20 Å2
3----0.059 Å2
Refinement stepCycle: LAST / Resolution: 2.304→43.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 26 243 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132353
X-RAY DIFFRACTIONr_bond_other_d0.0360.0181995
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6293207
X-RAY DIFFRACTIONr_angle_other_deg2.371.5794668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39723.435131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53715386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.376159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022656
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02527
X-RAY DIFFRACTIONr_nbd_refined0.2130.2576
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.21948
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21072
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2177
X-RAY DIFFRACTIONr_metal_ion_refined0.090.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.214
X-RAY DIFFRACTIONr_nbd_other0.2290.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0780.29
X-RAY DIFFRACTIONr_mcbond_it3.7543.2971086
X-RAY DIFFRACTIONr_mcbond_other3.7423.2921085
X-RAY DIFFRACTIONr_mcangle_it5.7774.9271364
X-RAY DIFFRACTIONr_mcangle_other5.7754.9331365
X-RAY DIFFRACTIONr_scbond_it5.0153.7911267
X-RAY DIFFRACTIONr_scbond_other5.0133.7921268
X-RAY DIFFRACTIONr_scangle_it7.6915.4691837
X-RAY DIFFRACTIONr_scangle_other7.6895.471838
X-RAY DIFFRACTIONr_lrange_it12.20839.8742912
X-RAY DIFFRACTIONr_lrange_other12.20139.662878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.304-2.3630.324760.251474X-RAY DIFFRACTION96.9962
2.363-2.4280.345740.2311495X-RAY DIFFRACTION100
2.428-2.4980.229820.2121427X-RAY DIFFRACTION100
2.498-2.5750.205700.2031410X-RAY DIFFRACTION100
2.575-2.6590.254700.2031370X-RAY DIFFRACTION100
2.659-2.7530.247810.2041306X-RAY DIFFRACTION100
2.753-2.8560.262700.181276X-RAY DIFFRACTION100
2.856-2.9730.239670.1911221X-RAY DIFFRACTION100
2.973-3.1040.253680.1821173X-RAY DIFFRACTION100
3.104-3.2550.231560.1851140X-RAY DIFFRACTION100
3.255-3.4310.214640.1921072X-RAY DIFFRACTION100
3.431-3.6380.213520.2171027X-RAY DIFFRACTION99.815
3.638-3.8880.317480.255974X-RAY DIFFRACTION99.7073
3.888-4.1980.137530.155889X-RAY DIFFRACTION99.6825
4.198-4.5970.15500.134834X-RAY DIFFRACTION100
4.597-5.1360.157390.138765X-RAY DIFFRACTION100
5.136-5.9230.196460.142671X-RAY DIFFRACTION100
5.923-7.2350.19360.175587X-RAY DIFFRACTION100
7.235-10.1560.178260.136462X-RAY DIFFRACTION100
10.156-43.9710.243130.238288X-RAY DIFFRACTION98.366

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