+Open data
-Basic information
Entry | Database: PDB / ID: 5mbk | ||||||
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Title | Structure of a bacterial light-regulated adenylyl cylcase | ||||||
Components | Beta subunit of photoactivated adenylyl cyclase | ||||||
Keywords | LYASE / BLUF / adenylyl cyclase / photoreceptor / optogenetics | ||||||
Function / homology | Function and homology information cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Beggiatoa sp. PS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Photoactivation Mechanism of a Bacterial Light-Regulated Adenylyl Cyclase. Authors: Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mbk.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mbk.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/5mbk ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mbk | HTTPS FTP |
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-Related structure data
Related structure data | 5m27SC 5m2aC 5mbbC 5mbcC 5mbdC 5mbeC 5mbgC 5mbhC 5mbjC 5nbyC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40110.441 Da / Num. of mol.: 1 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC / Mutation: Y7F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beggiatoa sp. PS (bacteria) / Gene: BGP_1043 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7BT71 | ||
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#2: Chemical | ChemComp-ATP / | ||
#3: Chemical | #4: 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: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1 M Na-HEPES pH 7.0, 20 % w/v PEG 3350; soak in 50mM Tris-HCl pH 7.6, 115 mM MgCl2, 48 mM ATP, 35% (w/v) PEG 3350 before cryo-cooling |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→45.9 Å / Num. obs: 17359 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M27 Resolution: 2.4→45.88 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.67 Å2 / Biso mean: 63.5584 Å2 / Biso min: 20.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→45.88 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: 5 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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