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- PDB-2g5r: Crystal structure of Siglec-7 in complex with methyl-9-(aminooxal... -

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Basic information

Entry
Database: PDB / ID: 2g5r
TitleCrystal structure of Siglec-7 in complex with methyl-9-(aminooxalyl-amino)-9-deoxyNeu5Ac (oxamido-Neu5Ac)
ComponentsSialic acid-binding Ig-like lectin 7
KeywordsCELL ADHESION / Siglec / sialic acid / sialoside
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-like domain superfamily ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CYSTEINE / Chem-NXD / Sialic acid-binding Ig-like lectin 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAttrill, H. / Crocker, P.R. / van Aalten, D.M.
CitationJournal: Biochem.J. / Year: 2006
Title: The structure of siglec-7 in complex with sialosides: leads for rational structure-based inhibitor design.
Authors: Attrill, H. / Takazawa, H. / Witt, S. / Kelm, S. / Isecke, R. / Brossmer, R. / Ando, T. / Ishida, H. / Kiso, M. / Crocker, P.R. / van Aalten, D.M.
History
DepositionFeb 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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 15, 2023Group: Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,3914
Polymers14,6551
Non-polymers7363
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.928, 52.928, 93.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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-7 / QA79 membrane protein / Adhesion inhibitory receptor molecule 1 / AIRM-1 / p75 / D-siglec / CDw328 antigen


Mass: 14655.292 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEF / Cell (production host): CHO Lec1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9Y286
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NXD / methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / METHYL 5-(ACETYLAMINO)-9-{[AMINO(OXO)ACETYL]AMINO}-3,5,9-TRIDEOXY-D-GLYCERO-ALPHA-D-GLUCO-NON-2-ULOPYRANOSIDONIC ACID / ALPHA METHYL -9-(AMINOOXALYL-AMINO)-9-DEOXYNEU5AC / OXAMIDO-NEU5AC / methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 5-acetamido-9-{[amino(oxo)acetyl]amino}-3,5,9-trideoxy-D-glycero-galacto-non-2-ulosidonic acid


Type: D-saccharide / Mass: 393.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H23N3O10
#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 4000, 0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 17748 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2 / % possible all: 78.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Siglec-7, APO, 1o7S

1o7s


Resolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.803 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 893 5 %RANDOM
Rwork0.213 ---
all0.214 ---
obs0.214 17691 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 48 102 1054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021975
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9611321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275111
X-RAY DIFFRACTIONr_chiral_restr0.0970.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02743
X-RAY DIFFRACTIONr_nbd_refined0.1860.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.214
X-RAY DIFFRACTIONr_mcbond_it1.773571
X-RAY DIFFRACTIONr_mcangle_it2.8633.2912
X-RAY DIFFRACTIONr_scbond_it2.4484404
X-RAY DIFFRACTIONr_scangle_it3.3113.5409
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.234 59
Rwork0.27 933
obs-992
Refinement TLS params.Method: refined / Origin x: 10.7764 Å / Origin y: 10.127 Å / Origin z: 19.8213 Å
111213212223313233
T0.1391 Å20.0239 Å20.0478 Å2-0.0042 Å20.0098 Å2--0.0648 Å2
L0.6945 °20.1996 °2-0.3042 °2-1.7583 °2-1.6745 °2--3.1111 °2
S0.0604 Å °0.0186 Å °-0.0241 Å °0.3748 Å °0.0953 Å °0.1108 Å °-0.4243 Å °-0.0939 Å °-0.1556 Å °

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