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- PDB-3t3a: Crystal structure of H107R mutant of extracellular domain of mous... -

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Basic information

Entry
Database: PDB / ID: 3t3a
TitleCrystal structure of H107R mutant of extracellular domain of mouse receptor NKR-P1A
ComponentsKiller cell lectin-like receptor subfamily B member 1A
KeywordsSIGNALING PROTEIN / C-type lectin-like domain / domain swapping / twinning / natural killer cell receptor / transmembrane 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: 2.3 Å
AuthorsKolenko, P. / Rozbesky, D. / Bezouska, K. / Hasek, J. / Dohnalek, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 A resolution.
Authors: Kolenko, P. / Rozbesky, D. / Vanek, O. / Bezouska, K. / Hasek, J. / Dohnalek, J.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,3415
Polymers32,0562
Non-polymers2853
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Killer cell lectin-like receptor subfamily B member 1A
B: Killer cell lectin-like receptor subfamily B member 1A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,68110
Polymers64,1114
Non-polymers5706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area11230 Å2
ΔGint-83 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.741, 64.741, 156.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

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


Mass: 16027.820 Da / Num. of mol.: 2 / Fragment: Extracellular domain (UNP residues 89-227) / Mutation: H107R
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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.3M ammonium phosphate, 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: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2009 / Details: 2 mirrors and a double-crystal monochromator
RadiationMonochromator: KMC-1, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.861
11-H, K, -L20.139
ReflectionResolution: 2.3→60 Å / Num. all: 14227 / Num. obs: 14227 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 7.5 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.427.50.5463.420641100
7.27-45.787.30.03139.5467199.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0116refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M9Z

3m9z


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0 / SU B: 2.411 / SU ML: 0.062 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: CCP4 stereochemistry library, version 6.1.3
Details: INTENSITY-BASED TWIN REFINEMENT, ALPHA(TWIN) 14%, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflectionSelection details
Rfree0.2157 708 RANDOM
Rwork0.1879 --
all0.1908 14227 -
obs0.1908 14227 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.893 Å2
Baniso -1Baniso -2Baniso -3
1-11.03 Å20 Å20 Å2
2--11.03 Å20 Å2
3----22.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 15 56 2016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211999
X-RAY DIFFRACTIONr_bond_other_d0.0010.021337
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9362705
X-RAY DIFFRACTIONr_angle_other_deg0.90433258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41225.588102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45915360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9431510
X-RAY DIFFRACTIONr_chiral_restr0.0970.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 54 -
Rwork0.211 961 -
obs--98.54 %

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