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- PDB-3m9z: Crystal Structure of extracellular domain of mouse NKR-P1A -

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Basic information

Entry
Database: PDB / ID: 3m9z
TitleCrystal Structure of extracellular domain of mouse NKR-P1A
ComponentsKiller cell lectin-like receptor subfamily B member 1A
KeywordsSIGNALING PROTEIN / C-type lectin-like domain / domain swapping / disulfide bond / receptor / transmembrane protein / natural killer cell receptor
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / signaling receptor activity / carbohydrate binding / cell surface / plasma membrane
Similarity search - Function
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
PHOSPHATE ION / Killer cell lectin-like receptor subfamily B member 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKolenko, P. / Rozbesky, D. / Bezouska, K. / Hasek, J. / Dohnalek, J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Molecular architecture of mouse activating NKR-P1 receptors.
Authors: Kolenko, P. / Rozbesky, D. / Vanek, O. / Kopecky, V. / Hofbauerova, K. / Novak, P. / Pompach, P. / Hasek, J. / Skalova, T. / Bezouska, K. / Dohnalek, J.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Killer cell lectin-like receptor subfamily B member 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1042
Polymers16,0091
Non-polymers951
Water2,000111
1
A: Killer cell lectin-like receptor subfamily B member 1A
hetero molecules

A: Killer cell lectin-like receptor subfamily B member 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2074
Polymers32,0182
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_465-x-1,-y+1,z1
Buried area3760 Å2
ΔGint-35 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.912, 59.912, 159.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1002-

HOH

21A-1105-

HOH

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Components

#1: Protein Killer cell lectin-like receptor subfamily B member 1A / NKR-P1A / Natural killer cell surface protein P1-2 / NKR-P1 2 / NKR-P1.7 / Lymphocyte antigen 55A / ...NKR-P1A / Natural killer cell surface protein P1-2 / NKR-P1 2 / NKR-P1.7 / Lymphocyte antigen 55A / Ly-55A / CD161 antigen-like family member A


Mass: 16008.773 Da / Num. of mol.: 1
Fragment: C-TYPE LECTIN-LIKE EXTRACELLULAR DOMAIN (UNP residues 89 to 227)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Klrb1a, Ly55, Ly55a, Nkrp1a / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3) RIL / References: UniProt: P27811
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.3M Ammonium phosphate, not buffered, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2009 / Details: MIRRORS, Microdiffractometer MD2
RadiationMonochromator: Si 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 16416 / % possible obs: 99.7 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999 / Redundancy: 7.4 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2319 / % possible all: 99

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E87

1e87


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 1.995 / SU ML: 0.065 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / Stereochemistry target values: CCP4 STEREOCHEMICAL LIBRARY
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; MAXIMUM LIKELIHOOD REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.23927 829 5 %RANDOM
Rwork0.19481 ---
all0.19696 16396 --
obs0.19696 16396 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 5 111 1121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211050
X-RAY DIFFRACTIONr_bond_other_d0.0010.02694
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9361430
X-RAY DIFFRACTIONr_angle_other_deg0.9231700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24225.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74715186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.775154
X-RAY DIFFRACTIONr_chiral_restr0.1080.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02206
X-RAY DIFFRACTIONr_mcbond_it1.3311.5623
X-RAY DIFFRACTIONr_mcbond_other0.3341.5255
X-RAY DIFFRACTIONr_mcangle_it2.35621008
X-RAY DIFFRACTIONr_scbond_it2.6493427
X-RAY DIFFRACTIONr_scangle_it3.8334.5419
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 55 -
Rwork0.326 1147 -
obs-1147 98.3 %

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