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- PDB-1kou: Crystal Structure of the Photoactive Yellow Protein Reconstituted... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kou | ||||||
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Title | Crystal Structure of the Photoactive Yellow Protein Reconstituted with Caffeic Acid at 1.16 A Resolution | ||||||
![]() | PHOTOACTIVE YELLOW PROTEIN | ||||||
![]() | PHOTOSYNTHESIS / photoreceptor | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Aalten, D.M.F. / Crielaard, W. / Hellingwerf, K.J. / Joshua-Tor, L. | ||||||
![]() | ![]() Title: Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution. Authors: van Aalten, D.M. / Crielaard, W. / Hellingwerf, K.J. / Joshua-Tor, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.5 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450 KB | Display | ![]() |
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Full document | ![]() | 450.4 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2phyS 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-DHC / |
#3: Chemical | ChemComp-NBU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.54 Å3/Da / Density % sol: 20.2 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→15 Å / Num. obs: 36609 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.16→1.2 Å / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3352 / % possible all: 89.4 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 333681 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 89.4 % / Num. unique obs: 3352 / Rmerge(I) obs: 0.546 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PHY Resolution: 1.16→8 Å / Num. parameters: 9856 / Num. restraintsaints: 12084 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 20.24 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1 Å / Num. disordered residues: 5 / Occupancy sum hydrogen: 862 / Occupancy sum non hydrogen: 1069 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.162 / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.162 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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