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- PDB-2dli: KILLER IMMUNOGLOBULIN RECEPTOR 2DL2,TRIGONAL FORM -

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Basic information

Entry
Database: PDB / ID: 2dli
TitleKILLER IMMUNOGLOBULIN RECEPTOR 2DL2,TRIGONAL FORM
ComponentsPROTEIN (MHC CLASS I NK CELL RECEPTOR PRECURSOR)
KeywordsIMMUNE SYSTEM / KIR / NATURAL KILLER RECEPTOR / INHIBITORY RECEPTOR / IMMUNOGLOBULIN
Function / homology
Function and homology information


immune response-regulating signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 2DL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSun, P.D. / Snyder, G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of the HLA-Cw3 allotype-specific killer cell inhibitory receptor KIR2DL2
Authors: Snyder, G.A. / Brooks, A.G. / Sun, P.D.
History
DepositionMar 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MHC CLASS I NK CELL RECEPTOR PRECURSOR)


Theoretical massNumber of molelcules
Total (without water)21,7261
Polymers21,7261
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.300, 91.300, 61.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN (MHC CLASS I NK CELL RECEPTOR PRECURSOR) / P58 NATURAL KILLER CELL RECEPTOR


Mass: 21726.369 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR HLA-CW3 RECOGNITION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER / Cellular location: SURFACE / Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P43627
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1250 mMcalcium acetate1reservoir
26 %PEG80001reservoir
333 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.9→10 Å / Num. obs: 6169 / % possible obs: 90 % / Redundancy: 3 % / Rsym value: 0.063 / Net I/σ(I): 13
Reflection shellResolution: 2.9→3 Å / Rsym value: 0.24 / % possible all: 75
Reflection
*PLUS
% possible obs: 90.3 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 75.4 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NKR

1nkr


Resolution: 2.9→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.331 -5 %RANDOM
Rwork0.227 ---
obs-5690 90 %-
Displacement parametersBiso mean: 64 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 0 10 1531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 64 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3

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