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- PDB-4nfd: Structure of PILR L108W mutant in complex with sialic acid -

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Basic information

Entry
Database: PDB / ID: 4nfd
TitleStructure of PILR L108W mutant in complex with sialic acid
ComponentsPaired immunoglobulin-like type 2 receptor beta
KeywordsIMMUNE SYSTEM / IgV-like / immune-related activation receptor / CD99 / sialic acid / cell surface
Function / homology
Function and homology information


activation of transmembrane receptor protein tyrosine kinase activity / MHC class I protein binding / cell surface receptor protein tyrosine kinase signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane
Similarity search - Function
Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Paired immunoglobulin-like type 2 receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.708 Å
AuthorsLu, Q. / Lu, G. / Qi, J. / Li, Y. / Zhang, Y. / Wang, H. / Fan, Z. / Yan, J. / Gao, G.F.
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 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: 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

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Assembly

Deposited unit
A: Paired immunoglobulin-like type 2 receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4302
Polymers14,1211
Non-polymers3091
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.580, 39.571, 41.481
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Paired immunoglobulin-like type 2 receptor beta / Activating receptor PILR-beta / Cell surface receptor FDFACT


Mass: 14121.013 Da / Num. of mol.: 1 / Fragment: UNP residues 32-150 / Mutation: L109W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDFACT, PILR, PILRB, PP1551 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKJ0
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 1.4M sodium citrate tribasic dehydrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 12120 / Num. obs: 11851 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 15.14
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.922 / Num. unique all: 988 / Rsym value: 0.347 / % possible all: 82.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NFB

4nfb


Resolution: 1.708→41.479 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 566 4.78 %Random
Rwork0.1706 ---
obs0.1725 11832 99 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.429 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5847 Å2-0 Å24.1054 Å2
2---4.6627 Å2-0 Å2
3---10.2474 Å2
Refinement stepCycle: LAST / Resolution: 1.708→41.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms998 0 21 108 1127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011072
X-RAY DIFFRACTIONf_angle_d1.141456
X-RAY DIFFRACTIONf_dihedral_angle_d13.364388
X-RAY DIFFRACTIONf_chiral_restr0.085151
X-RAY DIFFRACTIONf_plane_restr0.006185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.708-1.88040.25681560.2113274698
1.8804-2.15250.22411250.16582833100
2.1525-2.71180.24261400.17552839100
2.7118-41.49090.17721450.1597284898
Refinement TLS params.Method: refined / Origin x: 9.3252 Å / Origin y: 1.3773 Å / Origin z: 15.027 Å
111213212223313233
T0.0564 Å20.0003 Å20.0018 Å2-0.0599 Å20.0017 Å2--0.066 Å2
L0.0109 °2-0.0096 °20.001 °2-0.0197 °2-0.0003 °2--0.0294 °2
S-0.0036 Å °0.0044 Å °0.0167 Å °0.0103 Å °-0.0063 Å °-0.0205 Å °-0.024 Å °-0.0104 Å °-0.0136 Å °
Refinement TLS groupSelection details: all

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