+Open data
-Basic information
Entry | Database: PDB / ID: 2d01 | ||||||
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Title | Wild Type Photoactive Yellow Protein, P65 Form | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / PAS / LOV / GAF-DOMAINS / 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: 1.34 Å | ||||||
Authors | Shimizu, N. / Kamikubo, H. / Yamazaki, Y. / Imamoto, Y. / Kataoka, M. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pK(a) Regulation in Photoactive Yellow Protein Authors: Shimizu, N. / Kamikubo, H. / Yamazaki, Y. / Imamoto, Y. / Kataoka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d01.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d01.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d01_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 2d01_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 2d01_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2d01_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/2d01 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/2d01 | HTTPS FTP |
-Related structure data
Related structure data | 2d02C 2phyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Halorhodospira halophila (bacteria) / Gene: PYP / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P16113 |
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#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2004 / Details: bending magnet |
Radiation | Monochromator: fixed-exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→20.09 Å / Num. obs: 23170 / % possible obs: 99.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 11 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 9.09 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PHY Resolution: 1.34→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.817 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.989 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.34 Å / Num. reflection Rwork: 1706 / Total num. of bins used: 20 |