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- PDB-5xso: Crystal structure of full-length FixJ from B. japonicum crystalli... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xso | ||||||
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Title | Crystal structure of full-length FixJ from B. japonicum crystallized in space group C2221 | ||||||
![]() | Response regulator FixJ | ||||||
![]() | DNA BINDING PROTEIN / Response Regulater / FixJ/NarL Family / Full-length / unphosphorylated monomeric state | ||||||
Function / homology | ![]() Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nishizono, Y. / Hisano, T. / Sawai, H. / Shiro, Y. / Nakamura, H. / Wright, G.S.A. / Saeki, A. / Hikima, T. / Yamamoto, M. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
![]() | ![]() Title: Architecture of the complete oxygen-sensing FixL-FixJ two-component signal transduction system. Authors: Wright, G.S.A. / Saeki, A. / Hikima, T. / Nishizono, Y. / Hisano, T. / Kamaya, M. / Nukina, K. / Nishitani, H. / Nakamura, H. / Yamamoto, M. / Antonyuk, S.V. / Hasnain, S.S. / Shiro, Y. / Sawai, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
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PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19.4 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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Unit cell |
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Components
#1: Protein | Mass: 23355.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.96 % Description: The entry contains friedel pairs in I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG 8000, PEG 1000, sodium formate, glycerol, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 53635 / % possible obs: 99.5 % / Redundancy: 14.3 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1502 / CC1/2: 0.836 / Rpim(I) all: 0.262 / Rsym value: 0.832 / % possible all: 93.5 |
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Processing
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Refinement | Resolution: 1.778→39.674 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML Details: The entry contains friedel pairs in I_plus/minus columns
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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: 1.778→39.674 Å
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Refine LS restraints |
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LS refinement shell |
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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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