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- PDB-1od9: N-terminal of Sialoadhesin in complex with Me-a-9-N-benzoyl-amino... -

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Basic information

Entry
Database: PDB / ID: 1od9
TitleN-terminal of Sialoadhesin in complex with Me-a-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ compound)
ComponentsSIALOADHESIN
KeywordsLECTIN/IMMUNE SYSTEM / IMMUNE SYSTEM / IMMUNOGLOBULIN SUPERFAMILY / CARBOHYDRATE BINDING / SIGLEC / INHIBITOR DESIGN / LECTIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of T cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / endocytosis / carbohydrate binding / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-BND / Sialoadhesin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZaccai, N.R. / Maenaka, K. / Maenaka, T. / Crocker, P.R. / Brossmer, R. / Kelm, S. / Jones, E.Y.
CitationJournal: Structure / Year: 2003
Title: Structure-Guided Design of Sialic Acid-Based Siglec Inhibitors and Crystallographic Analysis in Complex with Sialoadhesin
Authors: Zaccai, N.R. / Maenaka, K. / Maenaka, T. / Crocker, P.R. / Brossmer, R. / Kelm, S. / Jones, E.Y.
History
DepositionFeb 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

Downloads & links

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Assembly

Deposited unit
A: SIALOADHESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8423
Polymers13,3191
Non-polymers5222
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.860, 67.860, 69.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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.: 1
Fragment: DOMAIN ONE, IG-LIKE V-TYPE DOMAIN, RESIDUES 20-138
Source method: isolated from a genetically manipulated source
Details: BOUND TO ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC, COORDINATE SYSTEM ORIGX ORIGX MATRIX (M) ORIGX VECTOR (V)
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: CHO CELL STABLE EXPRESSION WITH PEE14 PLASMID / Plasmid: PEE14 / Cell line (production host): CHO CELL / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q62230
#2: Sugar ChemComp-BND / methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC / methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 5-acetamido-3,5,9-trideoxy-9-[(phenylcarbonyl)amino]-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide / Mass: 426.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N2O9
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS A MACROPHAGE-RESTRICTED ADHESION MOLECULE THAT MEDIATES SIALIC-ACID DEPENDENT BINDING TO ...THIS IS A MACROPHAGE-RESTRICTED ADHESION MOLECULE THAT MEDIATES SIALIC-ACID DEPENDENT BINDING TO LYMPHOCYTES, OTHER EFFECTORS INCLUDE GRANULOCYTES, MONOCYTES, NATURAL KILLER CELLS AND B-CELLS MEMBER OF THE IMMUNOGLOBULINS SUPERFAMILY CONTAINING IG- AND V-TYPE DOMAINS.
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: 2.54 Å3/Da / Density % sol: 52 %
Crystal growpH: 4.6
Details: 1+1 DROP WITH 22.5 % (W/V) PEG 4000, 10 MM DTT, 0.18M AMMONIUM SULFATE, 0.09M SODIUM ACETATE PH 4.6,25MM BENZ COMPOUND
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mMBENZ1drop
210 mg/mlprotein1drop
310 mMHEPES1droppH7.5
410 mMdithiothreitol1drop
50.18 Mammonium sulfate1reservoir
60.09 Msodium acetate1reservoirpH4.6
722.5 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 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: 9849 / % possible obs: 99.9 % / Observed criterion σ(I): -1.5 / Redundancy: 11.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.4
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. measured all: 116504 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.2

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Processing

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

1qfo


Resolution: 2.1→19.72 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 254519.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.253 512 5.3 %RANDOM
Rwork0.209 ---
obs0.209 9667 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.8331 Å2 / ksol: 0.345172 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20 Å2
2---2.64 Å20 Å2
3---5.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-6 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 35 71 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
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_it3.581
X-RAY DIFFRACTIONc_mcangle_it4.31
X-RAY DIFFRACTIONc_scbond_it5.81.5
X-RAY DIFFRACTIONc_scangle_it6.821.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 81 5.5 %
Rwork0.284 1384 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3BENZYL2.PARAMBENZYL2.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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