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- PDB-1nkr: INHIBITORY RECEPTOR (P58-CL42) FOR HUMAN NATURAL KILLER CELLS -

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Basic information

Entry
Database: PDB / ID: 1nkr
TitleINHIBITORY RECEPTOR (P58-CL42) FOR HUMAN NATURAL KILLER CELLS
ComponentsP58-CL42 KIR
KeywordsINHIBITORY RECEPTOR / NATURAL KILLER CELLS / IMMUNOLOGICAL RECEPTORS / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


natural killer cell inhibitory signaling pathway / immune response-regulating signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / immune response / 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 2DL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsFan, Q.R. / Mosyak, L. / Winter, C.C. / Wagtmann, N. / Long, E.O. / Wiley, D.C.
CitationJournal: Nature / Year: 1997
Title: Structure of the inhibitory receptor for human natural killer cells resembles haematopoietic receptors.
Authors: Fan, Q.R. / Mosyak, L. / Winter, C.C. / Wagtmann, N. / Long, E.O. / Wiley, D.C.
History
DepositionJun 24, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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: P58-CL42 KIR


Theoretical massNumber of molelcules
Total (without water)22,2011
Polymers22,2011
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.360, 92.360, 46.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein P58-CL42 KIR / KILLER CELL INHIBITORY RECEPTOR


Mass: 22200.902 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER CELLS / Cell line: BL21 / Plasmid: PLM1 / Cellular location (production host): INCLUSION BODY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P43626
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.8 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.7
Details: PROTEIN WAS CRYSTALLIZED FROM 0.55 M (NH4)2HPO4, 50 MM SODIUM CITRATE, PH 5.4, FINAL PH 7.7. CRYSTALS WERE HARVESTED IN 1.5 M (NH4)2HPO4, 50 MM SODIUM CITRATE, PH 5.4, FINAL PH 7.7; THEN ...Details: PROTEIN WAS CRYSTALLIZED FROM 0.55 M (NH4)2HPO4, 50 MM SODIUM CITRATE, PH 5.4, FINAL PH 7.7. CRYSTALS WERE HARVESTED IN 1.5 M (NH4)2HPO4, 50 MM SODIUM CITRATE, PH 5.4, FINAL PH 7.7; THEN SOAKED IN 1.5 M (NH4)2HPO4, 50 MM SODIUM CITRATE, PH 5.4, 25% GLYCEROL, FINAL PH 7.7, AND FLASH-COOLED WITH LIQUID NITROGEN.
PH range: 5.4-7.7
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.55 Mammonium phosphate11
250 mMsodium citrate11

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: HORIZONTALLY BENT SI (111), ASYMMETRICALLY CUT CRYSTALS
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→16 Å / Num. obs: 25065 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4 / Rsym value: 0.234 / % possible all: 97.8
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 97.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE STRUCTURE WAS INITIALLY REFINED AT 10-2.2 ANGSTROMS USING POSITIONAL REFINEMENT AND SIMULATED ANNEALING PROTOCOLS IN X-PLOR. THE RESOLUTION WAS THEN EXTENDED TO 1.7 ANGSTROMS. REFINEMENT ...Details: THE STRUCTURE WAS INITIALLY REFINED AT 10-2.2 ANGSTROMS USING POSITIONAL REFINEMENT AND SIMULATED ANNEALING PROTOCOLS IN X-PLOR. THE RESOLUTION WAS THEN EXTENDED TO 1.7 ANGSTROMS. REFINEMENT AT THIS STAGE INVOLVED SIMULATED ANNEALING FOLLOWED BY B-FACTOR REFINEMENT, WITH THE EXTENSIVE USE OF SIMULATED ANNEALING OMIT MAPS. THE FINAL MODEL OBTAINED FROM X-PLOR WAS AGAIN REFINED WITH REFMAC. THE FINAL REFINEMENT STATISTICS FROM REFMAC ARE SHOWN HERE.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2427 10 %RANDOM
Rwork0.227 ---
obs0.205 24473 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 211 1724
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d1.83

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