+Open data
-Basic information
Entry | Database: PDB / ID: 4hh8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of bovine butyrophilin | ||||||
Components | Butyrophilin subfamily 1 member A1 | ||||||
Keywords | PROTEIN BINDING / Immunoglobulin Fold / milk fat globule | ||||||
Function / homology | Function and homology information regulation of immune response / regulation of cytokine production / T cell receptor signaling pathway / membrane => GO:0016020 / external side of plasma membrane / signaling receptor binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Eichinger, A. / Skerra, A. | ||||||
Citation | Journal: To be Published Title: The extracellular region of bovine butyrophilin exhibits high structural similarity to human myelin oligodendrocyte glycoprotein Authors: Eichinger, A. / Neumaier, I. / Skerra, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hh8.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hh8.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hh8_validation.pdf.gz | 421.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4hh8_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 4hh8_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4hh8_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/4hh8 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hh8 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25279.395 Da / Num. of mol.: 1 / Mutation: C193A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: BTN, BTN1A1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P18892 |
---|---|
#2: Water | ChemComp-HOH / |
Sequence details | THE DIFFERENCES BETWEEN THE SEQUENCE OF THE SOLVED STRUCTURE AND THE DATABASE ENTRY P18892 ARISE ...THE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.5 M potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97973,0.97985,0.96863,0.99188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.9 % / Av σ(I) over netI: 14.1 / Number: 32994 / Rsym value: 0.033 / D res high: 2.8 Å / D res low: 59.188 Å / Num. obs: 8446 / % possible obs: 99.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→59.264 Å / Num. all: 15058 / Num. obs: 15058 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.059 / Net I/σ(I): 16.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: MAD |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.3→59.26 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.2848 / WRfactor Rwork: 0.2323 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8146 / SU B: 5.777 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2541 / SU Rfree: 0.2263 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.254 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.5 Å2 / Biso mean: 42.1194 Å2 / Biso min: 21.09 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→59.26 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
|