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- PDB-3cad: Crystal structure of Natural Killer Cell Receptor, Ly49G -

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Basic information

Entry
Database: PDB / ID: 3cad
TitleCrystal structure of Natural Killer Cell Receptor, Ly49G
ComponentsLectin-related NK cell receptor LY49G1
KeywordsUNKNOWN FUNCTION / Ly49G / C-type lectin-like domain / natural killer receptor domain
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / external side of plasma membrane / plasma membrane
Similarity search - Function
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) ...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
Killer cell lectin-like receptor 7 / Lectin-related NK cell receptor LY49G1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCho, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular Architecture of the Major Histocompatibility Complex Class I-binding Site of Ly49 Natural Killer Cell Receptors.
Authors: Deng, L. / Cho, S. / Malchiodi, E.L. / Kerzic, M.C. / Dam, J. / Mariuzza, R.A.
History
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin-related NK cell receptor LY49G1
B: Lectin-related NK cell receptor LY49G1


Theoretical massNumber of molelcules
Total (without water)29,1512
Polymers29,1512
Non-polymers00
Water1,26170
1
A: Lectin-related NK cell receptor LY49G1


Theoretical massNumber of molelcules
Total (without water)14,5761
Polymers14,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lectin-related NK cell receptor LY49G1


Theoretical massNumber of molelcules
Total (without water)14,5761
Polymers14,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Lectin-related NK cell receptor LY49G1

A: Lectin-related NK cell receptor LY49G1


Theoretical massNumber of molelcules
Total (without water)29,1512
Polymers29,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1590 Å2
ΔGint-19.2 kcal/mol
Surface area14160 Å2
MethodPISA
4
B: Lectin-related NK cell receptor LY49G1

B: Lectin-related NK cell receptor LY49G1


Theoretical massNumber of molelcules
Total (without water)29,1512
Polymers29,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area1910 Å2
ΔGint-21.2 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.378, 56.196, 33.761
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-25-

HOH

21B-67-

HOH

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Components

#1: Protein Lectin-related NK cell receptor LY49G1


Mass: 14575.711 Da / Num. of mol.: 2 / Fragment: Ly49G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klra7 / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JHV6, UniProt: Q60654*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (weight/volume) PEG 4000, 0.1 mM Tris-HCl (pH 8.5), and 0.2 M MgCl2, 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: Feb 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 9945 / Num. obs: 8105 / % possible obs: 81.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.1 / % possible all: 45

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 30.243 / SU ML: 0.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28636 327 4.7 %RANDOM
Rwork0.227 ---
obs0.22971 6632 90.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.266 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å20 Å21.13 Å2
2--11.97 Å20 Å2
3----5.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 0 70 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9422811
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9545246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.93624.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.70115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.273158
X-RAY DIFFRACTIONr_chiral_restr0.220.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021557
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3710.21244
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3610.21369
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2980.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4190.296
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8961.51304
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.17221971
X-RAY DIFFRACTIONr_scbond_it4.69831018
X-RAY DIFFRACTIONr_scangle_it6.2034.5840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 19 -
Rwork0.31 327 -
obs--62.12 %
Refinement TLS params.Method: refined / Origin x: 34.2285 Å / Origin y: 20.6076 Å / Origin z: -7.7637 Å
111213212223313233
T0.1321 Å20.0334 Å20.0116 Å2-0.2254 Å20.0409 Å2--0.1264 Å2
L3.4762 °20.7597 °2-1.005 °2-0.2381 °2-0.1686 °2--0.8072 °2
S-0.0216 Å °0.0348 Å °-0.0838 Å °-0.0235 Å °-0.044 Å °-0.0031 Å °0.083 Å °0.0416 Å °0.0656 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA140 - 2623 - 125
2X-RAY DIFFRACTION1BB - A140 - 2593 - 122

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