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- PDB-3rs1: Mouse C-type lectin-related protein Clrg -

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Basic information

Entry
Database: PDB / ID: 3rs1
TitleMouse C-type lectin-related protein Clrg
ComponentsC-type lectin domain family 2 member I
KeywordsIMMUNE SYSTEM / C-type lectin-like / ligand of NK receptor / natural killer cell receptors / Surface of activated T lymphocytes
Function / homology
Function and homology information


positive regulation of immunological synapse formation / regulation of interleukin-2 production / membrane raft assembly / regulation of actin filament polymerization / natural killer cell lectin-like receptor binding / regulation of T cell proliferation / receptor clustering / negative regulation of osteoclast differentiation / transmembrane signaling receptor activity / T cell receptor signaling pathway ...positive regulation of immunological synapse formation / regulation of interleukin-2 production / membrane raft assembly / regulation of actin filament polymerization / natural killer cell lectin-like receptor binding / regulation of T cell proliferation / receptor clustering / negative regulation of osteoclast differentiation / transmembrane signaling receptor activity / T cell receptor signaling pathway / carbohydrate binding / membrane => GO:0016020 / external side of plasma membrane / cell surface
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / 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 2 member I
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSkalova, T. / Dohnalek, J. / Duskova, J. / Stepankova, A. / Koval, T. / Hasek, J. / Kotynkova, K. / Vanek, O. / Bezouska, K.
CitationJournal: J.Immunol. / Year: 2012
Title: Mouse Clr-g, a Ligand for NK Cell Activation Receptor NKR-P1F: Crystal Structure and Biophysical Properties.
Authors: Skalova, T. / Kotynkova, K. / Duskova, J. / Hasek, J. / Kovai, T. / Kolenko, P. / Novak, P. / Man, P. / Hanc, P. / Vanek, O. / Bezouska, K. / Dohnalek, J.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-type lectin domain family 2 member I
B: C-type lectin domain family 2 member I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8903
Polymers28,8542
Non-polymers351
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-14 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.310, 61.380, 32.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe values for the buried, surface area and the gain in the solvent free energy reported in remark 350 are from the as is analysis of the PISA server.

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Components

#1: Protein C-type lectin domain family 2 member I / C-type lectin-related protein DCL1 / C-type lectin-related protein G / Clr-g / Lymphoid-derived C- ...C-type lectin-related protein DCL1 / C-type lectin-related protein G / Clr-g / Lymphoid-derived C-type lectin-1 / LCL-1 / Osteoclast inhibitory lectin-related protein 2 / Ocil-related protein 2


Mass: 14427.196 Da / Num. of mol.: 2 / Fragment: Extracellular domain (UNP residues 85-206) / Mutation: I85M, C148S
Source method: isolated from a genetically manipulated source
Details: Refolded from inclusion bodies using commercially available iFOLD2 kit (Merck)
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Clec2i, Clrg, Dcl1, Ocilrp2 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) Gold / References: UniProt: Q9WVF9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 293 K / Method: spontaneous crystallization / pH: 7.5
Details: spontaneous crystallization on tube wall; buffer: 10 mM HEPES, pH 7.5, 100 mM NaCl and 1 mM NaN3, 2.3 mg/ml, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2010
RadiationMonochromator: KMC-1, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 18158 / Num. obs: 17372 / % possible obs: 96 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Redundancy: 5.6 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.5 / Num. unique all: 891 / % possible all: 90

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HUP

3hup


Resolution: 1.94→28.39 Å / Cor.coef. Fo:Fc: 0.941 / SU B: 2.878 / SU ML: 0.083 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): -1000 / Stereochemistry target values: CCP4 monomer library
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.268 (FREE R = 0.3630 FOR THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.268 (FREE R = 0.3630 FOR THE HIGHEST RESOLUTION SHELL) FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (887 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
Rwork0.18463 ---
all0.18641 17346 --
obs0.18641 16459 95.59 %-
Rfree---random
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--1.93 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.94→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 1 256 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212125
X-RAY DIFFRACTIONr_bond_other_d0.0010.021478
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.8992877
X-RAY DIFFRACTIONr_angle_other_deg0.86133537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55323.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3461516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7971.51224
X-RAY DIFFRACTIONr_mcbond_other0.1941.5498
X-RAY DIFFRACTIONr_mcangle_it1.44421960
X-RAY DIFFRACTIONr_scbond_it2.1643901
X-RAY DIFFRACTIONr_scangle_it3.3664.5913
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.241 1148 -
obs-1087 87.57 %

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