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Yorodumi- PDB-6g1y: Crystal structure of the photosensory core module (PCM) of a bath... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g1y | ||||||
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Title | Crystal structure of the photosensory core module (PCM) of a bathy phytochrome from Agrobacterium fabrum in the Pfr state. | ||||||
Components | (Bacteriophytochrome protein) x 2 | ||||||
Keywords | SIGNALING PROTEIN / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIN CHROMOPHORE / PHOTOISOMERIZATION / SIGNAL TRANSDUCTION / PFR STATE / LIGHT ADAPTATION / BATHY PHYTOCHROME / METHYLATION / PHOTOSENSORY CORE MODULE | ||||||
Function / homology | Function and homology information protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay signal transduction system / photoreceptor activity / regulation of DNA-templated transcription / ATP binding Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Schmidt, A. / Qureshi, B.M. / Scheerer, P. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural snapshot of a bacterial phytochrome in its functional intermediate state. Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / ...Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / Krauss, N. / Lamparter, T. / Hildebrandt, P. / Scheerer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g1y.cif.gz | 404.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g1y.ent.gz | 332 KB | Display | PDB format |
PDBx/mmJSON format | 6g1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g1y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6g1y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6g1y_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 6g1y_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g1y ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g1y | HTTPS FTP |
-Related structure data
Related structure data | 6g1zC 6g20C 3c2wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 56490.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81 | ||
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#2: Protein | Mass: 56503.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81 | ||
#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: 2.68 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: MPD, VAPOR DIFFUSION, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 2, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.09 Å / Num. obs: 42806 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.187 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.622 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C2W Resolution: 2.5→45.09 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 23.656 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R Free: 0.268 / 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: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.09 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.57 Å / Total num. of bins used: 20
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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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