+Open data
-Basic information
Entry | Database: PDB / ID: 4xb4 | ||||||
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Title | Structure of the N-terminal domain of OCP binding canthaxanthin | ||||||
Components | Orange carotenoid-binding protein | ||||||
Keywords | Carotenoid binding protein / photoprotection | ||||||
Function / homology | Function and homology information light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.544 Å | ||||||
Authors | Kerfeld, C.A. / Sutter, M. / Leverenz, R.L. | ||||||
Citation | Journal: Science / Year: 2015 Title: PHOTOSYNTHESIS. A 12 angstrom carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection. Authors: Leverenz, R.L. / Sutter, M. / Wilson, A. / Gupta, S. / Thurotte, A. / Bourcier de Carbon, C. / Petzold, C.J. / Ralston, C. / Perreau, F. / 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 | 4xb4.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xb4.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 4xb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xb4_validation.pdf.gz | 762.3 KB | Display | wwPDB validaton report |
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Full document | 4xb4_full_validation.pdf.gz | 765.6 KB | Display | |
Data in XML | 4xb4_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 4xb4_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xb4 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xb4 | HTTPS FTP |
-Related structure data
Related structure data | 4xb5C 3mg1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16604.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1963 / Production host: Escherichia coli (E. coli) / References: UniProt: P74102 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 51.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM citric acid BIS-TRIS propane pH 5.5, 24% poly-ethylene glycol 3350 |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→39 Å / Num. obs: 46069 / % possible obs: 99.55 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.02469 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3147 / Mean I/σ(I) obs: 2.52 / % possible all: 96.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Truncated version of 3MG1 Resolution: 1.544→38.757 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.81 / 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: 1.544→38.757 Å
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Refine LS restraints |
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LS refinement shell |
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