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Open data
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Basic information
Entry | Database: PDB / ID: 1ncn | ||||||
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Title | the receptor-binding domain of human B7-2 | ||||||
![]() | T lymphocyte activation antigen CD86 | ||||||
![]() | IMMUNE SYSTEM / Ig V / beta strands | ||||||
Function / homology | ![]() positive regulation of lymphotoxin A production / CD40 signaling pathway / positive regulation of T-helper 2 cell differentiation / activation of protein kinase C activity / CD28 co-stimulation / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / CTLA4 inhibitory signaling / B cell activation / positive regulation of interleukin-4 production ...positive regulation of lymphotoxin A production / CD40 signaling pathway / positive regulation of T-helper 2 cell differentiation / activation of protein kinase C activity / CD28 co-stimulation / CD28 dependent Vav1 pathway / positive regulation of immunoglobulin production / CTLA4 inhibitory signaling / B cell activation / positive regulation of interleukin-4 production / Interleukin-10 signaling / CD28 dependent PI3K/Akt signaling / : / centriolar satellite / coreceptor activity / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / positive regulation of non-canonical NF-kappaB signal transduction / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / virus receptor activity / signaling receptor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / adaptive immune response / receptor ligand activity / cell surface receptor signaling pathway / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / cell surface / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Schwartz, J.D. / Almo, S.C. / Nathenson, S.G. | ||||||
![]() | ![]() Title: Crystal Structure of the Receptor-Binding Domain of Human B7-2: Insights into Organization and Signaling Authors: Zhang, X. / Schwartz, J.D. / Almo, S.C. / Nathenson, S.G. #1: ![]() Title: Expression, Refolding, Purification, Molecular Characterization, Crystallization, and Preliminary X-ray Analysis of the Receptor Binding Domain of Human B7-2 Authors: Zhang, X. / Schwartz, J.-C.D. / Almo, S.C. / Nathenson, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 40.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 437.7 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 12849.631 Da / Num. of mol.: 2 / Fragment: Ig V-type domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.18 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, NaAC, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: Zhang, X., (2002) PROTEIN EXPRESSION PURIF., 25, 105. | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→19.83 Å / Num. all: 5843 / Num. obs: 5843 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.2 Å2 / Limit h max: 20 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 21 / Limit l min: 0 / Observed criterion F max: 1489970.8 / Observed criterion F min: 41.08 | ||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 90.8 | ||||||||||||
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. obs: 11122 / % possible obs: 99.8 % / Num. measured all: 44045 / Rmerge(I) obs: 0.095 | ||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 1110 / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 18.2567 Å2 / ksol: 0.37304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.42 Å2 / Biso mean: 21.94 Å2 / Biso min: 3.2 Å2
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Refine Biso | Class: polymer / Treatment: isotropic | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Rfactor Rfree: 0.327 |