+Open data
-Basic information
Entry | Database: PDB / ID: 5mbe | ||||||
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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 | 5mbe.cif.gz | 289.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mbe.ent.gz | 234.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mbe_validation.pdf.gz | 997.7 KB | Display | wwPDB validaton report |
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Full document | 5mbe_full_validation.pdf.gz | 1007.1 KB | Display | |
Data in XML | 5mbe_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 5mbe_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/5mbe ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mbe | HTTPS FTP |
-Related structure data
Related structure data | 5m27SC 5m2aC 5mbbC 5mbcC 5mbdC 5mbgC 5mbhC 5mbjC 5mbkC 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
#1: Protein | Mass: 40126.441 Da / Num. of mol.: 2 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beggiatoa sp. PS (bacteria) / Gene: BGP_1043 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7BT71 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M Na-MES pH 6.5, 0.6 M NaCl, 20 % w/v PEG 3350; 0.3 mM alpha,beta-methylene-ATP in drop |
-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: Apr 8, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.4→44.1 Å / Num. obs: 27155 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 43.63 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→44.082 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.68 Å2 / Biso mean: 69.0605 Å2 / Biso min: 21.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→44.082 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: 6
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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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