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- PDB-6bak: The structure of the Stigmatella aurantiaca phytochrome chromopho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bak | |||||||||||||||
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Title | The structure of the Stigmatella aurantiaca phytochrome chromophore binding domain T289H mutant | |||||||||||||||
![]() | Photoreceptor-histidine kinase BphP | |||||||||||||||
![]() | SIGNALING PROTEIN | |||||||||||||||
Function / homology | ![]() detection of visible light / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Schmidt, M. / Stojkovic, E. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome. Authors: Woitowich, N.C. / Halavaty, A.S. / Waltz, P. / Kupitz, C. / Valera, J. / Tracy, G. / Gallagher, K.D. / Claesson, E. / Nakane, T. / Pandey, S. / Nelson, G. / Tanaka, R. / Nango, E. / ...Authors: Woitowich, N.C. / Halavaty, A.S. / Waltz, P. / Kupitz, C. / Valera, J. / Tracy, G. / Gallagher, K.D. / Claesson, E. / Nakane, T. / Pandey, S. / Nelson, G. / Tanaka, R. / Nango, E. / Mizohata, E. / Owada, S. / Tono, K. / Joti, Y. / Nugent, A.C. / Patel, H. / Mapara, A. / Hopkins, J. / Duong, P. / Bizhga, D. / Kovaleva, S.E. / St Peter, R. / Hernandez, C.N. / Ozarowski, W.B. / Roy-Chowdhuri, S. / Yang, J.H. / Edlund, P. / Takala, H. / Ihalainen, J. / Brayshaw, J. / Norwood, T. / Poudyal, I. / Fromme, P. / Spence, J.C.H. / Moffat, K. / Westenhoff, S. / Schmidt, M. / Stojkovic, E.A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.2 KB | Display | ![]() |
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PDB format | ![]() | 62.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.7 KB | Display | ![]() |
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Full document | ![]() | 817.3 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bafC ![]() 6baoC ![]() 6bapC ![]() 6bayC ![]() 4rq9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 33820.625 Da / Num. of mol.: 1 Fragment: Phytochrome chromophore binding domain (UNP residues 16-318) Mutation: T289H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DW4/3-1 / Gene: STAUR_8015, STIAU_3396 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-BLR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.06 Å3/Da / Density % sol: 82.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.07 M sodium acetate trihydrate, pH 4.6, 1.4 M sodium formate, 30% w/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→100 Å / Num. obs: 71587 / % possible obs: 98 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.989 / Num. unique obs: 4196 / CC1/2: 0.416 / Rpim(I) all: 0.746 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4RQ9 Resolution: 1.92→23.423 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.77 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→23.423 Å
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Refine LS restraints |
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LS refinement shell |
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