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- PDB-4nfb: Structure of paired immunoglobulin-like type 2 receptor (PILR ) -

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Basic information

Entry
Database: PDB / ID: 4nfb
TitleStructure of paired immunoglobulin-like type 2 receptor (PILR )
ComponentsPaired immunoglobulin-like type 2 receptor alpha
KeywordsIMMUNE SYSTEM / IgV-like / immune-related inhibition receptor / HSV-1 gB / cell surface
Function / homology
Function and homology information


MHC class I protein binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Paired immunoglobulin-like type 2 receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLu, Q. / Lu, G. / Qi, J. / Li, Y. / Zhang, Y. / Wang, H. / Fan, Z. / Yan, J. / Gao, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: PILR alpha and PILR beta have a siglec fold and provide the basis of binding to sialic acid
Authors: Lu, Q. / Lu, G. / Qi, J. / Wang, H. / Xuan, Y. / Wang, Q. / Li, Y. / Zhang, Y. / Zheng, C. / Fan, Z. / Yan, J. / Gao, G.F.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired immunoglobulin-like type 2 receptor alpha


Theoretical massNumber of molelcules
Total (without water)14,0681
Polymers14,0681
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.544, 44.337, 57.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Paired immunoglobulin-like type 2 receptor alpha / Cell surface receptor FDF03 / Inhibitory receptor PILR-alpha


Mass: 14067.840 Da / Num. of mol.: 1 / Fragment: UNP residues 32-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PILR, PILRA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 1.83 Å3/Da / Density % sol: 32.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate tribasic dehydrate pH 5.6, 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 14159 / Num. obs: 13899 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 29.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.92 / Num. unique all: 1289 / Rsym value: 0.28 / % possible all: 92.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.07 Å / SU ML: 0.2 / σ(F): 0.13 / Phase error: 20.68 / Stereochemistry target values: ML
Details: The starting model is obtained by single isomorphous replacement with a iodine derivative data.
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 671 4.93 %Random
Rwork0.198 ---
obs0.1994 13610 96.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.577 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8691 Å2-0 Å2-0 Å2
2---5.0388 Å20 Å2
3----2.8302 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 130 1124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051024
X-RAY DIFFRACTIONf_angle_d0.9591385
X-RAY DIFFRACTIONf_dihedral_angle_d17.895370
X-RAY DIFFRACTIONf_chiral_restr0.065140
X-RAY DIFFRACTIONf_plane_restr0.003177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.72360.23921200.2073234689
1.7236-1.89710.25321270.1944255897
1.8971-2.17150.20641400.1846263599
2.1715-2.73570.23551310.19482690100
2.7357-33.07660.21521530.1948271097
Refinement TLS params.Method: refined / Origin x: 10.198 Å / Origin y: -8.3398 Å / Origin z: -6.4539 Å
111213212223313233
T0.0881 Å2-0.0036 Å20.0086 Å2-0.1003 Å20.002 Å2--0.0978 Å2
L0.7771 °2-0.3382 °2-0.2369 °2-0.6812 °20.1821 °2--1.3328 °2
S0.0154 Å °0.036 Å °-0.0148 Å °-0.0563 Å °-0.0328 Å °0.0046 Å °-0.1661 Å °-0.0038 Å °-0 Å °
Refinement TLS groupSelection details: all

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