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- PDB-1ja3: Crystal Structure of the Murine NK Cell Inhibitory Receptor Ly-49I -

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Basic information

Entry
Database: PDB / ID: 1ja3
TitleCrystal Structure of the Murine NK Cell Inhibitory Receptor Ly-49I
ComponentsMHC class I recognition receptor Ly49I
KeywordsIMMUNE SYSTEM / NK-CELL SURFACE GLYCOPROTEIN
Function / homology
Function and homology information


membrane => GO:0016020
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) / 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
MHC class I recognition receptor Ly49I
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDimasi, N. / Sawicki, W.M. / Reineck, L.A. / Li, Y. / Natarajan, K. / Murgulies, D.H. / Mariuzza, A.R.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the Ly49I natural killer cell receptor reveals variability in dimerization mode within the Ly49 family.
Authors: Dimasi, N. / Sawicki, M.W. / Reineck, L.A. / Li, Y. / Natarajan, K. / Margulies, D.H. / Mariuzza, R.A.
History
DepositionMay 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: MHC class I recognition receptor Ly49I
B: MHC class I recognition receptor Ly49I


Theoretical massNumber of molelcules
Total (without water)30,2492
Polymers30,2492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-17 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.733, 91.733, 89.584
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein MHC class I recognition receptor Ly49I


Mass: 15124.603 Da / Num. of mol.: 2 / Fragment: C-TYPE LECTIN-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: 129-J / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21CodonPlus / References: UniProt: Q9JHN9

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 8000 12%, NaCl 0.2 M, CHESS 0.1 M, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
212 %(w/v)PEG80001reservoir
30.2 M1reservoirNaCl
40.1 MCHES1reservoirpH9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2000 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection shellResolution: 3→50 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 0.24 / Num. unique all: 4739 / Rsym value: 0.061 / % possible all: 94.9
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 4739 / % possible obs: 94.9 % / Num. measured all: 65472 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 75.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.74

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO3

1qo3


Resolution: 3→29.72 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 234421.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 291 5.6 %RANDOM
Rwork0.333 ---
all-5162 --
obs-5162 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.54 Å2 / ksol: 0.262 e/Å3
Displacement parametersBiso mean: 73.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.75 Å214.47 Å20 Å2
2--7.75 Å20 Å2
3----15.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.66 Å
Luzzati d res low-5 Å
Luzzati sigma a1.21 Å1.09 Å
Refinement stepCycle: LAST / Resolution: 3→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 0 0 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_mcbond_it12.541.5
X-RAY DIFFRACTIONc_mcangle_it15.512
X-RAY DIFFRACTIONc_scbond_it3.082
X-RAY DIFFRACTIONc_scangle_it3.642.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.106 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.646 37 5.7 %
Rwork0.566 615 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. reflection obs: 4467 / Num. reflection Rfree: 272 / % reflection Rfree: 4.8 % / Rfactor Rfree: 0.2827 / Rfactor Rwork: 0.2787
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.15

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