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- PDB-6grs: Paired immunoglobulin-like receptor B (PirB) or Leukocyte immunog... -

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Basic information

Entry
Database: PDB / ID: 6grs
TitlePaired immunoglobulin-like receptor B (PirB) or Leukocyte immunoglobulin-like receptor subfamily B member 3 (LILRB3) full extracellular domain
ComponentsPaired immunoglobulin-like receptor B
KeywordsIMMUNE SYSTEM / neuronal growth inhibition / B cell down regulation
Function / homology
Function and homology information


cell surface receptor signaling pathway / membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Paired immunoglobulin-like receptor B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsVlieg, H.C. / Huizinga, E.G. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.012.002 Netherlands
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure and flexibility of the extracellular region of the PirB receptor.
Authors: Vlieg, H.C. / Huizinga, E.G. / Janssen, B.J.C.
History
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Paired immunoglobulin-like receptor B
B: Paired immunoglobulin-like receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5584
Polymers134,9132
Non-polymers6462
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint3 kcal/mol
Surface area59920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.690, 185.289, 99.080
Angle α, β, γ (deg.)90.00, 105.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Paired immunoglobulin-like receptor B


Mass: 67456.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pirb, Lilrb3 / Production host: Homo sapiens (human) / References: UniProt: Q8K4V6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.58 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.2 M LiCl, 12% PEG 6000m 0.1 M Citric acid buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→52.69 Å / Num. obs: 25778 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.949 / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.9
Reflection shellResolution: 3.4→3.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4683 / CC1/2: 0.586 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D3V, 4LLA

2d3v

4lla


Resolution: 3.4→52.686 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.35
RfactorNum. reflection% reflection
Rfree0.3075 1268 4.93 %
Rwork0.2558 --
obs0.2581 25708 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→52.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9167 0 42 0 9209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029472
X-RAY DIFFRACTIONf_angle_d0.60412893
X-RAY DIFFRACTIONf_dihedral_angle_d10.2425622
X-RAY DIFFRACTIONf_chiral_restr0.0441413
X-RAY DIFFRACTIONf_plane_restr0.0041637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.53630.37611540.33582692X-RAY DIFFRACTION99
3.5363-3.69720.42161710.33652681X-RAY DIFFRACTION98
3.6972-3.8920.36351220.32422709X-RAY DIFFRACTION98
3.892-4.13580.35941150.29142740X-RAY DIFFRACTION99
4.1358-4.4550.32871310.25172723X-RAY DIFFRACTION99
4.455-4.9030.2371220.22662716X-RAY DIFFRACTION98
4.903-5.61180.29691460.22672731X-RAY DIFFRACTION100
5.6118-7.06750.30691530.25792706X-RAY DIFFRACTION98
7.0675-52.69190.27261540.23052742X-RAY DIFFRACTION98

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