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- PDB-2zoh: X-ray Crystal Structure of Photoactive Yellow Protein, Wild type,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zoh | ||||||
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Title | X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K | ||||||
![]() | Photoactive yellow protein | ||||||
![]() | SIGNALING PROTEIN / PAS / LOV / PHOTORECEPTOR / LIGHT SENSOR / Chromophore / Photoreceptor protein / Receptor / Sensory transduction | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamaguchi, S. | ||||||
![]() | ![]() Title: Low-barrier hydrogen bond in photoactive yellow protein Authors: Yamaguchi, S. / Kamikubo, H. / Kurihara, K. / Kuroki, R. / Niimura, N. / Shimizu, N. / Yamazaki, Y. / Kataoka, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.4 KB | Display | ![]() |
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PDB format | ![]() | 50.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 433.3 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zoiC ![]() 2phyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop, microseeding / pH: 9 Details: AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.45 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→57.83 Å / Num. all: 28967 / Num. obs: 28967 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 10.11 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 7.3 / Num. unique all: 4176 / Rsym value: 0.356 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PHY Resolution: 1.25→50 Å / Num. parameters: 10353 / Num. restraintsaints: 13011 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1107 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→50 Å
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Refine LS restraints |
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