+Open data
-Basic information
Entry | Database: PDB / ID: 1ugu | ||||||
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Title | Crystal structure of PYP E46Q mutant | ||||||
Components | PHOTOACTIVE YELLOW PROTEIN | ||||||
Keywords | PHOTOSYNTHESIS / photorecepter | ||||||
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 | Sugishima, M. / Tanimoto, Y. / Hamada, N. / Tokunaga, F. / Fukuyama, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP. Authors: Sugishima, M. / Tanimoto, N. / Soda, K. / Hamada, N. / Tokunaga, F. / Fukuyama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ugu.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ugu.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ugu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/1ugu ftp://data.pdbj.org/pub/pdb/validation_reports/ug/1ugu | HTTPS FTP |
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-Related structure data
Related structure data | 2phyS 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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Details | The biological unit is monomer |
-Components
#1: Protein | Mass: 13887.591 Da / Num. of mol.: 1 / Mutation: E46Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Plasmid: pET16b / 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: 1.71 Å3/Da / Density % sol: 27.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.65 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 7, 2003 |
Radiation | Monochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→35 Å / Num. all: 33512 / Num. obs: 31902 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.037 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3170 / Rsym value: 0.368 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PHY Resolution: 1.2→34.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.685 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.293 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→34.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.202→1.233 Å / Total num. of bins used: 20 /
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