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- PDB-8dzx: Crystal structure of photoactive yellow protein (PYP); F96oCNF M1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dzx | |||||||||
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Title | Crystal structure of photoactive yellow protein (PYP); F96oCNF M100K construct | |||||||||
![]() | Photoactive yellow protein | |||||||||
![]() | SIGNALING PROTEIN / PHOTORECEPTOR | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kirsh, J.M. / Weaver, J.B. / Boxer, S.G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 54.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.1 KB | Display | ![]() |
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Full document | ![]() | 433.8 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dzuC ![]() 8dzyC ![]() 8e02C ![]() 8e03C ![]() 8e09C ![]() 8e1kC ![]() 8e1lC ![]() 1nwzS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 13911.569 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.85 % |
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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: ![]() ![]() ![]() |
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: 1.14→33.37 Å / Num. obs: 36321 / % possible obs: 98.6 % / Redundancy: 41.4 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.02 / Rrim(I) all: 0.13 / Net I/σ(I): 17.9 / Num. measured all: 1504406 / Scaling rejects: 1758 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 27.2 % / Rmerge(I) obs: 2.878 / Num. measured all: 37137 / Num. unique obs: 1367 / CC1/2: 0.641 / Rpim(I) all: 0.544 / Rrim(I) all: 2.933 / Net I/σ(I) obs: 1.3 / % possible all: 74.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NWZ Resolution: 1.14→33.37 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.47 / 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: 191.13 Å2 / Biso mean: 17.93 Å2 / Biso min: 7.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.14→33.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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