+Open data
-Basic information
Entry | Database: PDB / ID: 1a64 | ||||||
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Title | ENGINEERING A MISFOLDED FORM OF RAT CD2 | ||||||
Components | CD2 | ||||||
Keywords | DOMAIN 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 / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / 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 / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction / 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 | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 1a64.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a64.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a64_validation.pdf.gz | 370.5 KB | Display | wwPDB validaton report |
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Full document | 1a64_full_validation.pdf.gz | 375.6 KB | Display | |
Data in XML | 1a64_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1a64_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a64 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a64 | HTTPS FTP |
-Related structure data
Related structure data | 1a6pC 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: 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 / | |
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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: 2.01 Å3/Da / Density % sol: 32 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: 20% MPD, 200MM NACL, 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: 100 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: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNG Resolution: 2→15 Å / Data cutoff high absF: 0.001 / Data cutoff low absF: 1000000 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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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 |