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Yorodumi- PDB-8dzu: Crystal structure of photoactive yellow protein (PYP); F96oCNF M1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dzu | |||||||||
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Title | Crystal structure of photoactive yellow protein (PYP); F96oCNF M100H construct | |||||||||
Components | Photoactive yellow protein | |||||||||
Keywords | SIGNALING PROTEIN / PHOTORECEPTOR | |||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | |||||||||
Biological species | Halorhodospira halophila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | |||||||||
Authors | Kirsh, J.M. / Weaver, J.B. / Boxer, S.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Protic and Aprotic Interactions Systematically Perturbed and Mapped via MD and IR Spectroscopy Authors: Kirsh, J.M. / Kozuch, J. / Weaver, J.B. / Boxer, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dzu.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dzu.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 8dzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dzu_validation.pdf.gz | 643.5 KB | Display | wwPDB validaton report |
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Full document | 8dzu_full_validation.pdf.gz | 643.8 KB | Display | |
Data in XML | 8dzu_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 8dzu_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/8dzu ftp://data.pdbj.org/pub/pdb/validation_reports/dz/8dzu | HTTPS FTP |
-Related structure data
Related structure data | 8dzxC 8dzyC 8e02C 8e03C 8e09C 8e1kC 8e1lC 1nwzS 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: 13920.536 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) Strain (production host): DH10B / References: UniProt: P16113 |
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#2: Chemical | ChemComp-HC4 / |
#3: 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: 1.84 Å3/Da / Density % sol: 33.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.7126 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7126 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.04→33.25 Å / Num. obs: 48038 / % possible obs: 98.6 % / Redundancy: 41.1 % / Biso Wilson estimate: 9.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.023 / Rrim(I) all: 0.151 / Net I/σ(I): 14.3 / Num. measured all: 1976427 / Scaling rejects: 1759 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NWZ Resolution: 1.04→33.12 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.87 Å2 / Biso mean: 13.3411 Å2 / Biso min: 3.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.04→33.12 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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