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Yorodumi- PDB-5m85: Three-dimensional structure of the intermediate state of GAF3 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m85 | ||||||
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Title | Three-dimensional structure of the intermediate state of GAF3 from Slr1393 of Synechocystis sp. PCC6803 | ||||||
Components | Sensory transduction histidine kinase | ||||||
Keywords | TRANSFERASE / Cyanobacteriochrome / Phycocyanobilin chromophore / Photochromicity / bilin-binding GAF domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Xu, X.-L. / Zhao, K.-H. / Gaertner, W. / Hoeppner, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural elements regulating the photochromicity in a cyanobacteriochrome Authors: Xu, X.-L. / Hoeppner, A. / Wiebeler, C. / Zhao, K.-H. / Schapiro, I. / Gaertner, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m85.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m85.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 5m85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/5m85 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/5m85 | HTTPS FTP |
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-Related structure data
Related structure data | 5dfxSC 5dfyC 5m82C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24856.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Gene: slr1393 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73184 |
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-Non-polymers , 5 types, 79 molecules
#2: Chemical | ChemComp-CYC / | ||||
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#3: Chemical | ChemComp-3CX / ( | ||||
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1 M NaCl, 0.1 M LiSO4, 0.1 M CAPSO pH 9.5, 12% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.954 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 3, 2015 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→71.21 Å / Num. obs: 13390 / % possible obs: 99.6 % / Redundancy: 20.07 % / CC1/2: 1 / Rsym value: 0.063 / Net I/σ(I): 33.34 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 19.2 % / Mean I/σ(I) obs: 5.96 / CC1/2: 0.959 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DFX Resolution: 2.1→65.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.551 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.486 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→65.04 Å
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Refine LS restraints |
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