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- PDB-3h8n: Crystal Structure Analysis of KIR2DS4 -

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Basic information

Entry
Database: PDB / ID: 3h8n
TitleCrystal Structure Analysis of KIR2DS4
ComponentsKiller cell immunoglobulin-like receptor 2DS4
KeywordsIMMUNE SYSTEM / ligand-binding domains / Cell membrane / Disulfide bond / Glycoprotein / Immunoglobulin domain / Membrane / Polymorphism / Receptor / Transmembrane
Function / homology
Function and homology information


MHC class Ib protein binding / plasma membrane => GO:0005886 / DAP12 interactions / innate immune response / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Killer cell immunoglobulin-like receptor 2DS4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGraef, T. / Bushnell, D.A. / Parham, P.
CitationJournal: J.Exp.Med. / Year: 2009
Title: KIR2DS4 is a product of gene conversion with KIR3DL2 that introduced specificity for HLA-A*11 while diminishing avidity for HLA-C.
Authors: Graef, T. / Moesta, A.K. / Norman, P.J. / Abi-Rached, L. / Vago, L. / Older Aguilar, A.M. / Gleimer, M. / Hammond, J.A. / Guethlein, L.A. / Bushnell, D.A. / Robinson, P.J. / Parham, P.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Killer cell immunoglobulin-like receptor 2DS4


Theoretical massNumber of molelcules
Total (without water)21,5341
Polymers21,5341
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.232, 62.851, 65.934
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 Killer cell immunoglobulin-like receptor 2DS4 / MHC class I NK cell receptor / Natural killer-associated transcript 8 / NKAT-8 / P58 natural killer ...MHC class I NK cell receptor / Natural killer-associated transcript 8 / NKAT-8 / P58 natural killer cell receptor clone CL-39 / p58 NK receptor / CL-17 / CD158 antigen-like family member I


Mass: 21534.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD158I, KIR2DS4, KIR2DS4*0010101, KKA3, NKAT8 / Plasmid: pET-28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P43632
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.22 M Mg-Formate, 100 mM BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40.45 Å / Num. all: 7814 / Num. obs: 7795 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 44.26 Å2 / Rsym value: 0.05 / Net I/σ(I): 64.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10 % / Mean I/σ(I) obs: 9.7 / Num. unique all: 751 / Rsym value: 0.207 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-IceICEdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IM9

1im9


Resolution: 2.5→40.45 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.739 / SU ML: 0.48 / σ(F): 1.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 357 4.59 %RANDOM
Rwork0.238 ---
obs0.241 7778 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.131 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 88.15 Å2 / Biso mean: 45.112 Å2 / Biso min: 24 Å2
Baniso -1Baniso -2Baniso -3
1-3.744 Å20 Å2-0 Å2
2--7.791 Å2-0 Å2
3----11.535 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 53 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011562
X-RAY DIFFRACTIONf_angle_d1.3582122
X-RAY DIFFRACTIONf_chiral_restr0.093225
X-RAY DIFFRACTIONf_plane_restr0.013279
X-RAY DIFFRACTIONf_dihedral_angle_d19.234559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.8590.4021190.3042411253053
2.859-3.6010.3461140.252441255554
3.601-40.460.2271240.2122569269357

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