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Yorodumi- PDB-4jdq: Structure of the Fluorescence Recovery Protein from Synechocystis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jdq | ||||||
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Title | Structure of the Fluorescence Recovery Protein from Synechocystis sp PCC 6803, R60K mutant | ||||||
Components | Slr1964 protein | ||||||
Keywords | PROTEIN BINDING / photoprotection / non-photochemical quenching | ||||||
Function / homology | : / Fluorescence recovery protein / Photoprotection regulator fluorescence recovery protein / plasma membrane-derived thylakoid membrane / Fluorescence recovery protein Function and homology information | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å | ||||||
Authors | Sutter, M. / Kerfeld, C.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria. Authors: Sutter, M. / Wilson, A. / Leverenz, R.L. / Lopez-Igual, R. / Thurotte, A. / Salmeen, A.E. / Kirilovsky, D. / 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 | 4jdq.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jdq.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jdq_validation.pdf.gz | 467.2 KB | Display | wwPDB validaton report |
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Full document | 4jdq_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 4jdq_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4jdq_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/4jdq ftp://data.pdbj.org/pub/pdb/validation_reports/jd/4jdq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13186.942 Da / Num. of mol.: 6 / Mutation: R60K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1964 / Production host: Escherichia coli (E. coli) / References: UniProt: P74103 |
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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: 2.77 Å3/Da / Density % sol: 55.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 5% PEG-3350, 100mM Na-citrate, 2% tacsimate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00005 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2012 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00005 Å / Relative weight: 1 |
Reflection | Resolution: 3.51→39.09 Å / Num. all: 11816 / Num. obs: 11769 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.51→3.7 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.01539 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1625 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→39.089 Å / SU ML: 0.49 / σ(F): 1.33 / Phase error: 28.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.52→39.089 Å
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Refine LS restraints |
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LS refinement shell |
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