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- PDB-1a64: ENGINEERING A MISFOLDED FORM OF RAT CD2 -

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Basic information

Entry
Database: PDB / ID: 1a64
TitleENGINEERING A MISFOLDED FORM OF RAT CD2
ComponentsCD2
KeywordsDOMAIN SWAPPING / HINGE LOOP / OLIGOMER EVOLUTION
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 / signaling receptor binding / external side of plasma membrane / 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 norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurray, A.J. / Head, J.G. / Barker, J.J. / Brady, R.L.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Engineering an intertwined form of CD2 for stability and assembly.
Authors: Murray, A.J. / Head, J.G. / Barker, J.J. / Brady, R.L.
History
DepositionMar 5, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)21,7972
Polymers21,7972
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-38 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.720, 40.720, 105.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein CD2


Mass: 10898.259 Da / Num. of mol.: 2 / Fragment: DOMAIN 1 / Mutation: DEL(M46, K47)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: T-LYMPHOCYTES / Plasmid: PGEX-2T / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P08921
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.01 Å3/Da / Density % sol: 32 %
Crystal growpH: 4.6 / Details: 20% MPD, 200MM NACL, 0.1M NACO, PH 4.6
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %MPD1reservoir
2200 mM1reservoirNaCl
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 11660 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.09 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 19.87
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.15 / Rsym value: 0.271 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNG

1hng


Resolution: 2→15 Å / Data cutoff high absF: 0.001 / Data cutoff low absF: 1000000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 519 5 %RANDOM
Rwork0.2306 ---
obs0.2306 10920 97.8 %-
Displacement parametersBiso mean: 34.08 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 0 69 1553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.623
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3406 64 5 %
Rwork0.3433 1246 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TOPPAR:PARHCSDX.PROTOPPAR:TOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.3433

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