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- PDB-2bve: Structure of the N-terminal of Sialoadhesin in complex with 2-Phe... -

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Basic information

Entry
Database: PDB / ID: 2bve
TitleStructure of the N-terminal of Sialoadhesin in complex with 2-Phenyl- Prop5Ac
ComponentsSIALOADHESIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / LECTIN / SUPERFAMILY / CARBOHYDRATE BINDING / SIGLEC / INHIBITOR DESIGN / CELL ADHESION
Function / homology
Function and homology information


positive regulation of T cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / virion binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of type I interferon production / late endosome / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / early endosome / cell adhesion ...positive regulation of T cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / virion binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of type I interferon production / 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
Chem-PH5 / Sialoadhesin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZaccai, N.R. / May, A.P. / Robinson, R.C. / Burtnick, L.D. / Crocker, P. / Brossmer, R. / Kelm, S. / Jones, E.Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic and in Silico Analysis of the Sialoside-Binding Characteristics of the Siglec Sialoadhesin.
Authors: Zaccai, N.R. / May, A.P. / Robinson, R.C. / Burtnick, L.D. / Crocker, P. / Brossmer, R. / Kelm, S. / Jones, E.Y.
History
DepositionJun 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALOADHESIN
B: SIALOADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4654
Polymers26,6382
Non-polymers8272
Water2,054114
1
A: SIALOADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7332
Polymers13,3191
Non-polymers4131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIALOADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7332
Polymers13,3191
Non-polymers4131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.974, 70.961, 102.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35759, -0.82448, -0.43859), (-0.81737, 0.50348, -0.28004), (0.45171, 0.25835, -0.85394)
Vector: 34.01, 20.36, 12.51)

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Components

#1: Protein SIALOADHESIN / / SND1 / SIALIC ACID BINDING IG-LIKE LECTIN-1 / SIGLEC-1


Mass: 13319.107 Da / Num. of mol.: 2
Fragment: DOMAIN ONE, IG-LIKE V-TYPE DOMAIN, RESIDUES 20-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: MACROPHAGE / Plasmid: PEE14 PLASMID / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q62230
#2: Sugar ChemComp-PH5 / benzyl 3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / 2-PHENYL-PROP5AC / benzyl 3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / benzyl 3,5-dideoxy-5-(propanoylamino)-D-glycero-D-galacto-non-2-ulosidonic acid / benzyl 3,5-dideoxy-5-(propanoylamino)-D-glycero-galacto-non-2-ulosidonic acid / Benzyl group


Type: D-saccharide / Mass: 413.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27NO9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Description: DATA COLLECTED TO 2.1 ANGSTROM. STRUCTURE ONLY REFINED TO 2.2 ANGSTROM. MOLECULAR REPLACEMENT WITH ALL DATA BETWEEN 20 AND 3 ANGSTROM.
Crystal growpH: 5.6
Details: 1:1 DROP WITH 10MG/ML PROTEIN, 10MM DTT AND 24% PEG4000, 0.16MM MGCL2, 0.08 TRIS PH 8.5, 25MM COMPOUND

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 13244 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 4.95 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.45
Reflection shellResolution: 2.17→2.26 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 92

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFO

1qfo


Resolution: 2.2→19.72 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 96148.69 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27 607 5.1 %RANDOM
Rwork0.201 ---
obs0.201 11861 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0175 Å2 / ksol: 0.360159 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20 Å2
2--1.06 Å20 Å2
3----5.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 58 114 2036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
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: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 101 5.6 %
Rwork0.248 1696 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PROP_VERS11.PARAMPROP_VERS11.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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