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Yorodumi- PDB-5tz0: Structure of the Fremyella diplosiphon Fluorescence Recovery Protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tz0 | ||||||
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Title | Structure of the Fremyella diplosiphon Fluorescence Recovery Protein | ||||||
Components | Fluorescence Recovery Protein | ||||||
Keywords | PROTEIN BINDING / PHOTOPROTECTION / NON-PHOTOCHEMICAL QUENCHING | ||||||
Function / homology | Fluorescence recovery protein / Photoprotection regulator fluorescence recovery protein / thylakoid membrane / Uncharacterized protein Function and homology information | ||||||
Biological species | Tolypothrix sp. PCC 7601 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.025 Å | ||||||
Authors | Sutter, M. / Pawlowski, E.G. / Kerfeld, C.A. | ||||||
Citation | Journal: Nat Plants / Year: 2017 Title: Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria. Authors: Bao, H. / Melnicki, M.R. / Pawlowski, E.G. / Sutter, M. / Agostoni, M. / Lechno-Yossef, S. / Cai, F. / Montgomery, B.L. / Kerfeld, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tz0.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tz0.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 5tz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tz0_validation.pdf.gz | 426.6 KB | Display | wwPDB validaton report |
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Full document | 5tz0_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | 5tz0_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 5tz0_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/5tz0 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/5tz0 | HTTPS FTP |
-Related structure data
Related structure data | 4jdxS 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: 13530.222 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tolypothrix sp. PCC 7601 (bacteria) / Gene: FDUTEX481_08603 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6KMZ1 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 14% PEG-3000 0.1 M tri-sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→38.753 Å / Num. obs: 5519 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.02→3.19 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.754 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JDX Resolution: 3.025→38.753 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.025→38.753 Å
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Refine LS restraints |
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LS refinement shell |
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