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- PDB-3g8l: Crystal structure of murine natural killer cell receptor, Ly49L4 -

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Basic information

Entry
Database: PDB / ID: 3g8l
TitleCrystal structure of murine natural killer cell receptor, Ly49L4
ComponentsLectin-related NK cell receptor LY49L1
KeywordsIMMUNE SYSTEM / Natural Killer cell receptor / Ly49 / Receptor
Function / homology
Function and homology information


Ly49-like, N-terminal / Ly49-like protein, N-terminal region / 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 ...Ly49-like, N-terminal / Ly49-like protein, N-terminal region / 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
Lectin-related NK cell receptor LY49L4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCho, S.
CitationJournal: Immunity / Year: 2009
Title: Distinct conformations of Ly49 natural killer cell receptors mediate MHC class I recognition in trans and cis.
Authors: Back, J. / Malchiodi, E.L. / Cho, S. / Scarpellino, L. / Schneider, P. / Kerzic, M.C. / Mariuzza, R.A. / Held, W.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin-related NK cell receptor LY49L1
B: Lectin-related NK cell receptor LY49L1
C: Lectin-related NK cell receptor LY49L1
D: Lectin-related NK cell receptor LY49L1


Theoretical massNumber of molelcules
Total (without water)88,2814
Polymers88,2814
Non-polymers00
Water30617
1
A: Lectin-related NK cell receptor LY49L1
C: Lectin-related NK cell receptor LY49L1


Theoretical massNumber of molelcules
Total (without water)44,1402
Polymers44,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-26 kcal/mol
Surface area16430 Å2
MethodPISA
2
B: Lectin-related NK cell receptor LY49L1
D: Lectin-related NK cell receptor LY49L1


Theoretical massNumber of molelcules
Total (without water)44,1402
Polymers44,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-30 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.045, 78.045, 216.738
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein
Lectin-related NK cell receptor LY49L1


Mass: 22070.125 Da / Num. of mol.: 4
Fragment: C-type lectin-like domain with a part of the stalk (UNP residues 80-281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klra12, MOUSE / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CODONPLUS / References: UniProt: Q9JIP9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 25636 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Num. unique all: 1343 / Rsym value: 0.404 / % possible all: 50.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.503 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R: 0.942 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28719 1229 5.1 %RANDOM
Rwork0.22263 ---
obs0.2279 22705 90.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5145 0 0 17 5162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0450.0225290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.7561.9487121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9085618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37624.24250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.7415992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0641525
X-RAY DIFFRACTIONr_chiral_restr0.2390.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023945
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3740.22802
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3690.23486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.2269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.2127
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3940.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9061.53238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.19424970
X-RAY DIFFRACTIONr_scbond_it4.75232563
X-RAY DIFFRACTIONr_scangle_it6.3384.52151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.519 37 -
Rwork0.25 817 -
obs--44.41 %

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