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- PDB-3pyp: PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pyp | ||||||
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Title | PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE | ||||||
![]() | PHOTOACTIVE YELLOW PROTEIN | ||||||
![]() | PHOTORECEPTOR / LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Genick, U.K. / Soltis, S.M. / Kuhn, P. / Canestrelli, I.L. / Getzoff, E.D. | ||||||
![]() | ![]() Title: Structure at 0.85 A resolution of an early protein photocycle intermediate. Authors: Genick, U.K. / Soltis, S.M. / Kuhn, P. / Canestrelli, I.L. / Getzoff, E.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.2 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 KB | Display | ![]() |
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Full document | ![]() | 444.1 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13.1 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 on special symmetry positions |
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Components
#1: Protein | Mass: 13888.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THIOESTER LINKAGE BETWEEN THE SULFUR OF CYS 69 AND CARBOXY GROUP OF THE 4-HYDROXY CINNAMIC ACID CHROMOPHORE Source: (natural) ![]() |
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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: 1.8 Å3/Da / Density % sol: 32 % / Description: CRYSTALS IDENTICAL TO 2PHY | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 / Details: pH 4.8 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: used as seeds | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 149 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 6, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77 Å / Relative weight: 1 |
Reflection | Highest resolution: 0.85 Å / Num. obs: 84934 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 0.85→0.86 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.52 / % possible all: 87.1 |
Reflection | *PLUS Num. measured all: 561693 |
Reflection shell | *PLUS % possible obs: 87.1 % |
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Processing
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Refinement | Method to determine structure: SAME CRYSTAL LATTICE MOLECULAR REPLACEMENT Starting model: 2PHY Resolution: 0.85→50 Å / Num. parameters: 11379 / Num. restraintsaints: 15920 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: NUMBER OF PROTEIN AND SOLVENT ATOMS CONTAINS DUAL CONFORMERS
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 18 / Occupancy sum hydrogen: 943 / Occupancy sum non hydrogen: 1133 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→50 Å
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Refine LS restraints |
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