+Open data
-Basic information
Entry | Database: PDB / ID: 2qj5 | ||||||
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Title | PYP ultra-high resolution of a bacterial photoreceptor | ||||||
Components | Photoactive yellow protein | ||||||
Keywords | SIGNALING PROTEIN / PAS domain | ||||||
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: 1.2 Å | ||||||
Authors | Coureux, P.D. / Fan, Z.P. / Stojanoff, V. / Genick, U.K. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Picometer-scale conformational heterogeneity separates functional from nonfunctional States of a photoreceptor protein. Authors: Coureux, P.D. / Fan, Z.P. / Stojanoff, V. / Genick, U.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qj5.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qj5.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qj5_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 2qj5_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 2qj5_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2qj5_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qj5 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qj5 | HTTPS FTP |
-Related structure data
Related structure data | 2qj7C 1nwzS C: citing same article (ref.) S: Starting model for refinement |
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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 / Production host: Escherichia coli (E. coli) / 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: 2.03 Å3/Da / Density % sol: 39.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 39% PEG 3000, 50 mM Tris-HCl pH 9, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.85 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2005 Details: Si(111) channel cut monochromator Toroidal focusing mirror |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→40 Å / Num. obs: 32475 / Redundancy: 3.1 % / Rmerge(I) obs: 0.045 / Rsym value: 0.039 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1115 / Rsym value: 0.18 / % possible all: 71.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NWZ Resolution: 1.2→33.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.549 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.051 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.527 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→33.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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