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- PDB-1b6u: CRYSTAL STRUCTURE OF THE HUMAN KILLER CELL INHIBITORY RECEPTOR (K... -

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Basic information

Entry
Database: PDB / ID: 1b6u
TitleCRYSTAL STRUCTURE OF THE HUMAN KILLER CELL INHIBITORY RECEPTOR (KIR2DL3) SPECIFIC FOR HLA-CW3 RELATED ALLELES
ComponentsP58 KILLER CELL INHIBITORY RECEPTOR
KeywordsKILLER CELL INHIBITORY RECEPTOR / NATURAL KILLER CELL / HLA / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I (MHC CLASS I) / CELL SURFACE RECEPTOR / IMMUNOGLOBULIN SUPERFAMILY
Function / homology
Function and homology information


immune response-regulating signaling pathway / antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / immune response / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Killer cell immunoglobulin-like receptor 2DL3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMaenaka, K. / Juji, T. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of the human p58 killer cell inhibitory receptor (KIR2DL3) specific for HLA-Cw3-related MHC class I.
Authors: Maenaka, K. / Juji, T. / Stuart, D.I. / Jones, E.Y.
History
DepositionJan 18, 1999Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_wavelength_list
Revision 1.4Nov 20, 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

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Assembly

Deposited unit
A: P58 KILLER CELL INHIBITORY RECEPTOR


Theoretical massNumber of molelcules
Total (without water)28,1891
Polymers28,1891
Non-polymers00
Water00
1
A: P58 KILLER CELL INHIBITORY RECEPTOR

A: P58 KILLER CELL INHIBITORY RECEPTOR


Theoretical massNumber of molelcules
Total (without water)56,3782
Polymers56,3782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)95.400, 95.400, 130.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein P58 KILLER CELL INHIBITORY RECEPTOR / KIR2DL3


Mass: 28189.141 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CLONING BY PCR / Cell: NATURAL KILLER CELL / Cell line: BL21 / Cellular location: CELL SURFACE / Gene: NKAT2 / Plasmid: PKMATHNK2
Cellular location (production host): MEDIA AND PERIPLASMIC SPACE
Gene (production host): NKAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P43628
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: 3.05 Å3/Da / Density % sol: 60 % / Description: DATA WERE COLLECTED USING WEISSENBERG METHOD.
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, sitting drop
Details: protein solution is mixed in a 1:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 mMTris-HCl1drop
39-10 %PEG80001reservoir
450 mMHEPES1reservoir
58 %ethylene glycol1reservoir
60.5 %octyl-beta-glucoside1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 6281 / % possible obs: 84.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 4.7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 18460
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5refinement
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REFINED BY X-PLOR, REFMAC AND CN
RfactorNum. reflection% reflectionSelection details
Rfree0.32 354 5 %RANDOM
Rwork0.248 ---
obs0.248 5896 79.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-4.12 Å20 Å2
2---0.4 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 0 1541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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