+Open data
-Basic information
Entry | Database: PDB / ID: 2vfy | ||||||
---|---|---|---|---|---|---|---|
Title | AKAP18 delta central domain | ||||||
Components | AKAP18 DELTA | ||||||
Keywords | HYDROLASE / APO | ||||||
Function / homology | Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta Function and homology information | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Gold, M.G. / Smith, F.D. / Scott, J.D. / Barford, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Akap18 Contains a Phosphoesterase Domain that Binds AMP Authors: Gold, M.G. / Smith, F.D. / Scott, J.D. / Barford, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vfy.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vfy.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vfy_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2vfy_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 2vfy_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2vfy_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/2vfy ftp://data.pdbj.org/pub/pdb/validation_reports/vf/2vfy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23226.936 Da / Num. of mol.: 1 / Fragment: RESIDUES 88-292 Source method: isolated from a genetically manipulated source Details: 2H PHOSPHOESTERASE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 / Details: 0.1 M TRIS HCL PH 8, 10 % PEG 8K, 7 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9794 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 30, 2005 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→97.13 Å / Num. obs: 18073 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 2.73 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.8→97.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.656 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 31.55 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→97.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|