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- PDB-6lkr: Crystal structure of mouse DCAR2 CRD domain complex -

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Basic information

Entry
Database: PDB / ID: 6lkr
TitleCrystal structure of mouse DCAR2 CRD domain complex
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 / 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) ...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: 1.84 Å
AuthorsOmahdi, Z. / Horikawa, Y. / Toyonaga, K. / 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
DepositionDec 20, 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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)32,0765
Polymers31,7142
Non-polymers3623
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-24 kcal/mol
Surface area13310 Å2
Unit cell
Length a, b, c (Å)64.423, 72.068, 100.580
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-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.68 Å3/Da / Density % sol: 66.59 %
Crystal growTemperature: 293.4 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: BL45XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→48.03 Å / Num. obs: 77390 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 9.8
Reflection shellResolution: 1.84→1.95 Å / Num. unique obs: 12362 / CC1/2: 0.519

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LFJ

6lfj


Resolution: 1.84→48.03 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.49 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1884 3753 4.85 %
Rwork0.1718 73635 -
obs0.1726 77388 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.97 Å2 / Biso mean: 40.489 Å2 / Biso min: 20.3 Å2
Refinement stepCycle: final / Resolution: 1.84→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 21 235 2428
Biso mean--64.39 49.05 -
Num. residues----264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.870.35891320.3372565269794
1.87-1.890.37881440.311527902934100
1.89-1.920.30751380.280426682806100
1.92-1.950.25981400.267727642904100
1.95-1.970.2991410.258327192860100
1.97-2.010.26631420.240527322874100
2.01-2.040.26831400.24112705284599
2.04-2.070.21751410.22632725286698
2.07-2.110.26811410.22182729287099
2.11-2.150.26131450.203727682913100
2.15-2.20.21321370.196227082845100
2.2-2.240.19031410.189727512892100
2.24-2.30.21651390.185627632902100
2.3-2.350.22281390.192226972836100
2.35-2.420.17911450.180327662911100
2.42-2.490.21461380.1827292867100
2.49-2.570.20681400.18212721286199
2.57-2.660.22991290.17332711284099
2.66-2.770.17891410.179427242865100
2.77-2.890.2291340.177227502884100
2.89-3.040.20031360.164327572893100
3.05-3.240.16811390.164827422881100
3.24-3.490.16391420.155827152857100
3.49-3.840.17061380.14322726286499
3.84-4.390.12421340.133227402874100
4.39-5.530.14871370.134827362873100
5.53-48.030.16771400.16472734287499
Refinement TLS params.Method: refined / Origin x: -4.6982 Å / Origin y: 24.6444 Å / Origin z: -13.0386 Å
111213212223313233
T0.2367 Å20.0021 Å20.006 Å2-0.2512 Å2-0.0016 Å2--0.2434 Å2
L0.3294 °20.1343 °2-0.3244 °2-0.906 °2-0.6657 °2--0.8377 °2
S0.0242 Å °0.0336 Å °0.0326 Å °0.0243 Å °0.04 Å °0.0353 Å °-0.0399 Å °-0.0921 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA76 - 207
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB76 - 207
4X-RAY DIFFRACTION1allS2 - 246
5X-RAY DIFFRACTION1allC1 - 2

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