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- PDB-1hng: CRYSTAL STRUCTURE AT 2.8 ANGSTROMS RESOLUTION OF A SOLUBLE FORM O... -

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Basic information

Entry
Database: PDB / ID: 1hng
TitleCRYSTAL STRUCTURE AT 2.8 ANGSTROMS RESOLUTION OF A SOLUBLE FORM OF THE CELL ADHESION MOLECULE CD2
ComponentsCD2
KeywordsT LYMPHOCYTE ADHESION GLYCOPROTEIN
Function / homology
Function and homology information


natural killer cell activation / heterotypic cell-cell adhesion / natural killer cell mediated cytotoxicity / positive regulation of interleukin-8 production / cell-cell adhesion / receptor tyrosine kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction ...natural killer cell activation / heterotypic cell-cell adhesion / natural killer cell mediated cytotoxicity / positive regulation of interleukin-8 production / cell-cell adhesion / receptor tyrosine kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction / immune response / external side of plasma membrane / signaling receptor binding / protein kinase binding / cell surface / Golgi apparatus / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsJones, E.Y. / Davis, S.J. / Williams, A.F. / Harlos, K. / Stuart, D.I.
Citation
Journal: Nature / Year: 1992
Title: Crystal structure at 2.8 A resolution of a soluble form of the cell adhesion molecule CD2.
Authors: Jones, E.Y. / Davis, S.J. / Williams, A.F. / Harlos, K. / Stuart, D.I.
#1: Journal: To be Published
Title: Ligand Binding by the Immunoglobulin Superfamily Recognition Molecule Cd2 is Glycosylation Independent
Authors: Davis, S.J. / Davies, E.A. / Barclay, A.N. / Daenke, S. / Bodian, D.L. / Jones, E.Y. / Stuart, D.I. / Butters, T.D. / Dwek, R.A. / Van Der Merwe, P.A.
#2: Journal: Protein Eng. / Year: 1993
Title: Expression of Soluble Recombinant Glycoproteins with Predefined Glycosylation: Application to the Crystallization of the T-Cell Glycoprotein Cd2
Authors: Davis, S.J. / Puklavec, M.J. / Ashford, D.A. / Harlos, K. / Jones, E.Y. / Stuart, D.I. / Williams, A.F.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD2
B: CD2


Theoretical massNumber of molelcules
Total (without water)40,2762
Polymers40,2762
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)111.400, 111.400, 86.900
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 CD2


Mass: 20138.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Organ: OVARY / References: UniProt: P08921
Has protein modificationY
Nonpolymer detailsFOUR NAG (N-ACETYL GLUCOSAMINE) GROUPS AT ASN 67, 77, 84, AND 112 WERE NOT MODELED IN REFINEMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
225 mMTris1drop
3140 mM1dropNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 13432 / % possible obs: 96 %
Reflection
*PLUS
Num. measured all: 51452 / Rmerge(I) obs: 0.126

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→20 Å /
RfactorNum. reflection
Rwork0.215 -
obs0.215 13432
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 0 0 2796
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.015

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