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- PDB-3nou: Light-induced intermediate structure L3 of P. aeruginosa bacterio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nou | ||||||
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Title | Light-induced intermediate structure L3 of P. aeruginosa bacteriophytochrome | ||||||
![]() | Bacteriophytochrome | ||||||
![]() | SIGNALING PROTEIN / Intermediate structure | ||||||
Function / homology | ![]() osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yang, X. / Ren, Z. / Moffat, K. | ||||||
![]() | ![]() Title: Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome. Authors: Yang, X. / Ren, Z. / Kuk, J. / Moffat, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.2 KB | Display | ![]() |
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PDB format | ![]() | 83.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.4 KB | Display | ![]() |
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Full document | ![]() | 806.6 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nhqSC ![]() 3nopC ![]() 3notC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 56823.230 Da / Num. of mol.: 1 / Fragment: Photosensory Core Module Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-BLA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.7 Details: 10mg/ml protein, 0.45M ammonium phosphate, 0.1M Tris buffer, pH 7.7, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction |
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 12, 2008 | |||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.9→50 Å / Num. all: 134289 / Num. obs: 132947 / % possible obs: 99 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.106 |
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Processing
Software |
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Refinement | Method to determine structure: difference Fourier Method Starting model: PDB ENTRY 3NHQ Resolution: 3→50 Å / σ(F): 0 / σ(I): 0 Details: This cryo-trapped structure was determined based on difference Fourier method. The L1 (3NOP), L2(3NOT) and L3(3NOU) structures were refined jointly in real space against a set of (Flight- ...Details: This cryo-trapped structure was determined based on difference Fourier method. The L1 (3NOP), L2(3NOT) and L3(3NOU) structures were refined jointly in real space against a set of (Flight-Fdark) difference maps representing mixtures of the L1, L2 and L3 structures in variable relative concentrations using software DynamiX. DynamiX is a collection of software tools for analyzing dynamic crystallographic data developed by Zhong Ren. Algorithms and methods are described in Ren, Z et al. Resolution of structural heterogeneity in dynamic and static crystallography. Manuscript in preparation.
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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