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- PDB-1nko: Energetic and structural basis of sialylated oligosaccharide reco... -

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Basic information

Entry
Database: PDB / ID: 1nko
TitleEnergetic and structural basis of sialylated oligosaccharide recognition by the natural killer cell inhibitory receptor p75/AIRM1 or Siglec-7
ComponentsSialic acid binding Ig-like lectin 7
KeywordsIMMUNE SYSTEM / Immunoglobulin / Siglec7
Function / homology
Function and homology information


sialic acid binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / carbohydrate binding / cell adhesion / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Sialic acid-binding Ig-like lectin 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDimasi, N. / Attril, H. / van Aalten, D.M.F. / Moretta, L. / Biassoni, R. / Mariuzza, R.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the saccharide-binding domain of the human natural killer cell inhibitory receptor p75/AIRM1.
Authors: Dimasi, N. / Moretta, A. / Moretta, L. / Biassoni, R. / Mariuzza, R.A.
History
DepositionJan 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sialic acid binding Ig-like lectin 7


Theoretical massNumber of molelcules
Total (without water)15,2631
Polymers15,2631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.461, 49.715, 39.787
Angle α, β, γ (deg.)90.00, 113.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sialic acid binding Ig-like lectin 7 / Siglec-7 / QA79 membrane protein / Adhesion inhibitory receptor molecule-1 / AIRM-1 / p75 / D-siglec


Mass: 15262.995 Da / Num. of mol.: 1 / Fragment: N-terminal IgV-like domain residues 19-150 / Mutation: Q55D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC7 OR AIRM1 / Plasmid: p75-1D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9Y286
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.2
Details: PEG 4000 20%, NaCl 0.2 M, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 277 K / pH: 5.5 / Method: vapor diffusion, hanging drop / Details: Dimasi, N., (2003) Acta Crystallogr., D59, 1856.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
225 mMMES1droppH5.5
320 %(w/v)PEG80001reservoir
40.2 M1reservoirNaCl
50.1 Mphosphate-citrate1reservoirpH4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→15 Å / Num. obs: 19800 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.8 Å2
Reflection shellResolution: 1.45→15 Å / % possible all: 95.3
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 20819 / % possible obs: 89.3 % / Num. measured all: 238401 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Lowest resolution: 1.51 Å / % possible obs: 68.6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFO

1qfo


Resolution: 1.45→14.93 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 830 4.2 %RANDOM
Rwork0.277 ---
obs0.277 19760 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.3265 Å2 / ksol: 0.44952 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å20 Å2-3.37 Å2
2--3.91 Å20 Å2
3----0.9 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.45→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 0 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d28.4
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it3.491.5
X-RAY DIFFRACTIONc_mcangle_it4.832
X-RAY DIFFRACTIONc_scbond_it3.652
X-RAY DIFFRACTIONc_scangle_it4.612.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 104 4 %
Rwork0.378 2525 -
obs--76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 4 % / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17

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