+Open data
-Basic information
Entry | Database: PDB / ID: 1a6p | ||||||
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Title | ENGINEERING OF A MISFOLDED FORM OF CD2 | ||||||
Components | T-CELL SURFACE ANTIGEN CD2 | ||||||
Keywords | CELL ADHESION / DOMAIN SWAPPING / HINGE LOOP / OLIGOMER EVOLUTION / T LYMPHOCYTE ADHESION GLYCOPROTEIN | ||||||
Function / homology | Function and homology information natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / positive regulation of interleukin-8 production / cytoplasmic side of plasma membrane / cell-cell adhesion / receptor tyrosine kinase binding / : / cell-cell junction / positive regulation of type II interferon production ...natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / positive regulation of interleukin-8 production / cytoplasmic side of plasma membrane / cell-cell adhesion / receptor tyrosine kinase binding / : / cell-cell junction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / external side of plasma membrane / signaling receptor binding / protein kinase binding / Golgi apparatus / cell surface / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Murray, A.J. / Head, J.G. / Barker, J.J. / Brady, R.L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6p.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6p.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 1a6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6p ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6p | HTTPS FTP |
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-Related structure data
Related structure data | 1a64C 1a7bC 1hngS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10538.900 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 31.8 % | ||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: 20% PEG 4000, 5% GLYCEROL, 0.1M NACO, PH 4.6 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 10589 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 2.89 % / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.08→2.15 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.57 / Rsym value: 0.295 / % possible all: 99 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNG Resolution: 2.08→15 Å / Data cutoff high absF: 2.08 / Data cutoff low absF: 10 / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 20 - 29 IN BOTH CHAINS COMPRISE A FLEXIBLE LOOP REGION; HENCE THE B FACTORS ARE HIGH WITH POOR PACKING, AND SOME NON H-BOND DONORS IN THE AREA.
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Displacement parameters | Biso mean: 32.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.17 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
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Xplor file |
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