+Open data
-Basic information
Entry | Database: PDB / ID: 2vfl | ||||||
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Title | AKAP18 delta central domain - CMP | ||||||
Components | AKAP18 DELTA | ||||||
Keywords | HYDROLASE / APO / PHOSPHOESTERASE / CAMP / AKAP / PKA / SCAFFOLD / CMP | ||||||
Function / homology | Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta / CYTIDINE-5'-MONOPHOSPHATE Function and homology information | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vfl.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vfl.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/2vfl ftp://data.pdbj.org/pub/pdb/validation_reports/vf/2vfl | HTTPS FTP |
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-Related 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: 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 |
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#2: Chemical | ChemComp-C5P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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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 |
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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: 2.25→98.06 Å / Num. obs: 9559 / % possible obs: 99.5 % / Observed criterion σ(I): 2.5 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.2 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: APO STRUCTURE Resolution: 2.25→98.06 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.881 / SU B: 15.727 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 19.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→98.06 Å
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Refine LS restraints |
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