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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


positive regulation of interleukin-8 secretion / positive regulation of interferon-gamma secretion / heterotypic cell-cell adhesion / positive regulation of tumor necrosis factor production / T cell activation / cell-cell adhesion / receptor tyrosine kinase binding / protein self-association / membrane raft / external side of plasma membrane ...positive regulation of interleukin-8 secretion / positive regulation of interferon-gamma secretion / heterotypic cell-cell adhesion / positive regulation of tumor necrosis factor production / T cell activation / cell-cell adhesion / receptor tyrosine kinase binding / protein self-association / membrane raft / external side of plasma membrane / protein kinase binding / cell surface / protein homodimerization activity / protein-containing complex / integral component of membrane
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C2-set domain / Immunoglobulin-like domain superfamily / T-cell surface antigen CD2 / Immunoglobulin-like fold / Immunoglobulin C2-set
T-cell surface antigen CD2
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 10, 1994 / Release: Feb 7, 1995
RevisionDateData content typeGroupProviderType
1.0Feb 7, 1995Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD2
B: CD2


Theoretical massNumber of molelcules
Total (without water)40,2762
Polymers40,2762
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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/peptide 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
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

Crystal-ID: 1 / Sol-ID: drop

IDConc.Common nameChemical formula
117 mg/mlprotein
225 mMTris
3140 mMNaCl

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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
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.015

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