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- PDB-5j2s: NKR-P1B from Rattus norvegicus -

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Basic information

Entry
Database: PDB / ID: 5j2s
TitleNKR-P1B from Rattus norvegicus
ComponentsKiller cell lectin-like receptor subfamily B member 1B allele A
KeywordsIMMUNE SYSTEM / immune receptor / signaling protein
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
Killer cell lectin-like receptor subfamily B member 1B allele A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSkalova, T. / Vanek, O. / Blaha, J. / Duskova, J. / Hasek, J. / Koval, T. / Dohnalek, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation15-15181S Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
CitationJournal: To Be Published
Title: Structure of NKR-P1B from Rattus norvegicus
Authors: Vanek, O. / Skalova, T. / Blaha, J. / Duskova, J. / Hasek, J. / Koval, T. / Dohnalek, J.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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


Theoretical massNumber of molelcules
Total (without water)34,6604
Polymers33,4872
Non-polymers1,1732
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.721, 60.721, 76.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12N
22O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A14 - 135
2111B14 - 135
1121N511 - 513
2121O511 - 513

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(1, 0.000302, -0.000944), (0.000303, -0.999999, 0.000964), (-0.000944, -0.000964, -0.999999)-0.00235, -35.04614, -0.01758

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Components

#1: Protein Killer cell lectin-like receptor subfamily B member 1B allele A / CD161 antigen-like family member B / Natural killer cell surface protein NKR-P1B allele RNK/SD/BN/F344


Mass: 16743.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: natural killer cells / Gene: Klrb1b, Nkrp1b / Plasmid: pYD5
Details (production host): modified version of pTT5 plasmid (Durocher et al., NAR 2002)
Cell line (production host): HEK293S GnTI- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): human embryonic kidney / References: UniProt: A4KWA1
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.44 Å3/Da / Density % sol: 49.64 % / Description: cube 100x100x100 um
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 80 mM HEPES, pH 7.5, 20% (w/v) PEG3000, 20% (v/v) glycerol

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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: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→52.59 Å / Num. obs: 21405 / % possible obs: 100 % / Redundancy: 3.3 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YHF

2yhf


Resolution: 2→52.59 Å / Cor.coef. Fo:Fc: 0.955 / SU B: 4.675 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 677 3.2 %random selection
Rwork0.22134 ---
obs0.22134 21380 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.708 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å2-0 Å2
2---0.66 Å2-0 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 2→52.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 78 101 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022072
X-RAY DIFFRACTIONr_bond_other_d0.0030.021872
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.982814
X-RAY DIFFRACTIONr_angle_other_deg1.04334364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9015246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45925.68288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.076156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02448
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_it4.5755.175978
X-RAY DIFFRACTIONr_mcbond_other4.5695.171977
X-RAY DIFFRACTIONr_mcangle_it6.6297.7311220
X-RAY DIFFRACTIONr_mcangle_other6.6287.7361221
X-RAY DIFFRACTIONr_scbond_it4.6265.8021094
X-RAY DIFFRACTIONr_scbond_other4.6245.8041095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2588.5011593
X-RAY DIFFRACTIONr_long_range_B_refined9.62741.5542422
X-RAY DIFFRACTIONr_long_range_B_other9.59341.5232394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6540.89
22B681.01
LS refinement shellResolution: 1.997→2.049 Å
RfactorNum. reflection% reflection
Rfree0.348 44 4 %
Rwork0.313 1522 -
obs--97.31 %

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