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Open data
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Basic information
Entry | Database: PDB / ID: 1dck | ||||||
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Title | STRUCTURE OF UNPHOSPHORYLATED FIXJ-N COMPLEXED WITH MN2+ | ||||||
![]() | TRANSCRIPTIONAL REGULATORY PROTEIN FIXJ | ||||||
![]() | TRANSCRIPTION / DOUBLY WOUND FIVE-STRANDED BETA/ALPHA FOLD / NITROGEN FIXATION REGULATION | ||||||
Function / homology | ![]() nitrogen fixation / DNA-binding transcription activator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gouet, P. / Fabry, B. / Guillet, V. / Birck, C. / Mourey, L. / Kahn, D. / Samama, J.P. | ||||||
![]() | ![]() Title: Structural transitions in the FixJ receiver domain. Authors: Gouet, P. / Fabry, B. / Guillet, V. / Birck, C. / Mourey, L. / Kahn, D. / Samama, J.P. #1: ![]() Title: Conformational changes induced by phosphorylation of the FixJ receiver domain Authors: Birck, C. / Mourey, L. / Gouet, P. / Fabry, B. / Schumacher, J. / Rousseau, P. / Kahn, D. / Samama, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 668 KB | Display | ![]() |
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Full document | ![]() | 670.1 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13880.008 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN (RESIDUES 1-126) / Mutation: T2Q, A125L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-15P / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 35 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 4K | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 30 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 24325 / Num. obs: 13062 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.196 / % possible all: 57.7 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 87 % / Num. measured all: 24325 |
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Processing
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Refinement | Resolution: 2→14.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 701624.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.82 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→14.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.308 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.25 |