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- PDB-1qfp: N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) -

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Basic information

Entry
Database: PDB / ID: 1qfp
TitleN-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE)
ComponentsPROTEIN (SIALOADHESIN)
KeywordsIMMUNOGLOBULIN / IMMUNOGLOBULIN SUPERFAMILY / CARBOHYDRATE BINDING
Function / homology
Function and homology information


positive regulation of T cell apoptotic process / virion binding / positive regulation of extrinsic apoptotic signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsMay, A.P. / Robinson, R.C. / Burtnick, L. / Crocker, P.R. / Jones, E.Y.
CitationJournal: Mol.Cell / Year: 1998
Title: Crystal structure of the N-terminal domain of sialoadhesin in complex with 3' sialyllactose at 1.85 A resolution.
Authors: May, A.P. / Robinson, R.C. / Vinson, M. / Crocker, P.R. / Jones, E.Y.
History
DepositionApr 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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: PROTEIN (SIALOADHESIN)


Theoretical massNumber of molelcules
Total (without water)13,3191
Polymers13,3191
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)38.900, 38.900, 152.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein PROTEIN (SIALOADHESIN)


Mass: 13319.107 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SIALIC ACID-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PEE14 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q62230
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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5
Details: 16 % (W/V) PEG 4000, 8% (V/V) PROPAN-2-OL, 10 MM DTT, 80MM SODIUM HEPES PH 7.5, 5MG/ML PROTEIN
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225 mM3' sialyllactose 1drop
330 %(w/v)PEG40001reservoir
40.1 Msodium citrate1reservoir
50.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 3275 / Num. obs: 3275 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.8→2.97 Å / % possible all: 89.8
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS0.5refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.015 / Data cutoff high rms absF: 464034.24 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 350 10.7 %RANDOM
Rwork0.198 ---
all-3275 --
obs-3275 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.68 Å2 / ksol: 0.278 e/Å3
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.72 Å210.75 Å20 Å2
2--6.72 Å20 Å2
3----13.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms899 0 0 0 899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 51 9.8 %
Rwork0.276 468 -
obs--89.8 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor obs: 0.276

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