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Yorodumi- PDB-8a3u: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (symme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a3u | ||||||
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Title | Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (symmetrical variant, trigonal form with short c-axis) | ||||||
Components | Putative Sensory box protein,Sensor protein FixL | ||||||
Keywords | SIGNALING PROTEIN / LOV domain / PAS domain / Photocycle / Dimerization / Signaling blue light photoreceptor / sensory histidine kinase / chimeric / De Novo Protein | ||||||
Function / homology | Function and homology information histidine phosphotransfer kinase activity / nitrogen fixation / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida KT2440 (bacteria) Bradyrhizobium diazoefficiens USDA 110 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å | ||||||
Authors | Arinkin, V. / Batra-Safferling, R. / Granzin, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (symmetrical variant, trigonal form with short c-axis) Authors: Arinkin, V. / Batra-Safferling, R. / Granzin, J. / Krauss, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a3u.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a3u.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 8a3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/8a3u ftp://data.pdbj.org/pub/pdb/validation_reports/a3/8a3u | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43368.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; belongs to Q88JB0: 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120); belongs to P23222:141 (or 121 PDB-file)-EHQQTQ...AADEN-388 (or 368); UNP:Q88JB0 ...Details: His-Tag: 1-MGSSHHHHHHSSGLVPRGSH-20; belongs to Q88JB0: 21 (or 1 PDB-file)-(MSE)INA...YYIGIQRDVT-140 (or 120); belongs to P23222:141 (or 121 PDB-file)-EHQQTQ...AADEN-388 (or 368); UNP:Q88JB0 (UNP-numbering) 4-(MSE)INA...QRDVT-123; UNP:P23222 (UNP-numbering) 258 to C-Term. Expression system: because of SeMet: E.coli B834 (DE3). Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria), (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria) Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440, JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110 Gene: PP_2739, fixL, bll2760 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: Q88JB0, UniProt: P23222, histidine kinase |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-FMN / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10% PEG8K, 0.1M Citrate, 0.2M NaCl, 0.1M Ammonium Bromide, 1mM ATP, 2mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97916 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 13, 2015 |
Radiation | Monochromator: Silicon (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→45.65 Å / Num. obs: 13863 / % possible obs: 58.6 % / Redundancy: 20 % / Biso Wilson estimate: 75.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.027 / Rrim(I) all: 0.12 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.33→2.51 Å / Rmerge(I) obs: 2.26 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 693 / CC1/2: 0.48 / Rpim(I) all: 0.549 / % possible all: 14.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.33→45.65 Å / SU ML: 0.4343 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 40.4131 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The refinement was performed against F(+) and F(-). The number "Unique reflections" given above refers to the "NON-ANOMALOUS" reflections (13861 reflections). However, separating the ...Details: The refinement was performed against F(+) and F(-). The number "Unique reflections" given above refers to the "NON-ANOMALOUS" reflections (13861 reflections). However, separating the reflections on F(+) and F(-), the Phenix program gives a number of 26710 reflections for the refinement. The statistics (number of reflections) in resolution shells also refers to F(+) and F(-). Attention, these are very strong anisotropic data, so that the spherical completeness is relatively low.
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→45.65 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A
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