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- PDB-2dru: Crystal structure and binding properties of the CD2 and CD244 (2B... -

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Basic information

Entry
Database: PDB / ID: 2dru
TitleCrystal structure and binding properties of the CD2 and CD244 (2B4) binding protein, CD48
Componentschimera of CD48 antigen and T-cell surface antigen CD2
KeywordsIMMUNE SYSTEM / CD2 binding domain of CD48
Function / homology
Function and homology information


Cell surface interactions at the vascular wall / mast cell activation / natural killer cell activation / T cell activation / immune response / receptor ligand activity / membrane raft / external side of plasma membrane / signal transduction / protein-containing complex / extracellular region
Similarity search - Function
: / Immunoglobulin domain / 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 ...: / Immunoglobulin domain / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEvans, E.J. / Ikemizu, S. / Davis, S.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure and Binding Properties of the CD2 and CD244 (2B4)-binding Protein, CD48
Authors: Evans, E.J. / Castro, M.A.A. / O'Brien, R. / Kearney, A. / Walsh, H. / Sparks, L.M. / Tucknott, M.G. / Davies, E.A. / Carmo, A.M. / van der Merwe, P.A. / Stuart, D.I. / Jones, E.Y. / ...Authors: Evans, E.J. / Castro, M.A.A. / O'Brien, R. / Kearney, A. / Walsh, H. / Sparks, L.M. / Tucknott, M.G. / Davies, E.A. / Carmo, A.M. / van der Merwe, P.A. / Stuart, D.I. / Jones, E.Y. / Ladbury, J.E. / Ikemizu, S. / Davis, S.J.
History
DepositionJun 15, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 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 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimera of CD48 antigen and T-cell surface antigen CD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2669
Polymers21,1421
Non-polymers1,1248
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.780, 96.780, 126.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein chimera of CD48 antigen and T-cell surface antigen CD2


Mass: 21142.105 Da / Num. of mol.: 1 / Fragment: Domain 1, CD2 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1 / References: UniProt: P10252
#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.: 3
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M sodium HEPES, 1.5M lithium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.977 Å
DetectorDate: Feb 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 9426 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 49.5 Å2

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Processing

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

1ccz


Resolution: 2.6→24.2 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 440671.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 501 5.3 %RANDOM
Rwork0.214 ---
obs0.214 9400 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1525 Å2 / ksol: 0.390139 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.19 Å20 Å20 Å2
2--7.19 Å20 Å2
3----14.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 72 42 1595
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.661.5
X-RAY DIFFRACTIONc_mcangle_it4.332
X-RAY DIFFRACTIONc_scbond_it4.92
X-RAY DIFFRACTIONc_scangle_it6.942.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.461 71 4.7 %
Rwork0.376 1448 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4gol.pargol.top

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