+Open data
-Basic information
Entry | Database: PDB / ID: 7z9e | ||||||
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Title | Deinococcus radiodurans BphP PAS-GAF H260A/Y263F mutant | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / KINASE / PHOTOSENSOR / PHYTOCHROME | ||||||
Function / homology | Function and homology information osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å | ||||||
Authors | Takala, H. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Photochem Photobiol Sci / Year: 2022 Title: Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome. Authors: Lehtivuori, H. / Rumfeldt, J. / Mustalahti, S. / Kurkinen, S. / Takala, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z9e.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z9e.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 7z9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z9e_validation.pdf.gz | 880.5 KB | Display | wwPDB validaton report |
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Full document | 7z9e_full_validation.pdf.gz | 882.7 KB | Display | |
Data in XML | 7z9e_validation.xml.gz | 18 KB | Display | |
Data in CIF | 7z9e_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/7z9e ftp://data.pdbj.org/pub/pdb/validation_reports/z9/7z9e | HTTPS FTP |
-Related structure data
Related structure data | 7z9dC 2o9cS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37146.387 Da / Num. of mol.: 1 / Mutation: H260A, Y263F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: bphP, DR_A0050 / Plasmid: pET21B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-LBV / | #5: Water | ChemComp-HOH / | 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: 2.41 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 4.95 Details: sodium acetate, PEG 400, DTT, 2-methyl-2,4-pentanediol Temp details: cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 16, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→19.84 Å / Num. obs: 57357 / % possible obs: 97.1 % / Redundancy: 4.207 % / Biso Wilson estimate: 31.121 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.047 / Χ2: 0.852 / Net I/σ(I): 16.43 / Num. measured all: 241285 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O9C Resolution: 1.48→19.84 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 3.329 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0624 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.01 Å2 / Biso mean: 30.704 Å2 / Biso min: 12.29 Å2
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Refinement step | Cycle: final / Resolution: 1.48→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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