[English] 日本語
Yorodumi- PDB-5fcy: Structure of Anabaena (Nostoc) sp. PCC 7120 Red Carotenoid Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fcy | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Anabaena (Nostoc) sp. PCC 7120 Red Carotenoid Protein binding a mixture of carotenoids | ||||||
Components | Red carotenoid protein (RCP) | ||||||
Keywords | CARTENOID BINDING PROTEIN / carotenoid / photoprotection / cyanobacteria | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.508 Å | ||||||
Authors | Sutter, M. / Leverrenz, R.L. / Kerfeld, C.A. | ||||||
Citation | Journal: Mol Plant / Year: 2016 Title: Structure, Diversity, and Evolution of a New Family of Soluble Carotenoid-Binding Proteins in Cyanobacteria. Authors: Melnicki, M.R. / Leverenz, R.L. / Sutter, M. / Lopez-Igual, R. / Wilson, A. / Pawlowski, E.G. / Perreau, F. / Kirilovsky, D. / Kerfeld, C.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fcy.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fcy.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fcy_validation.pdf.gz | 625 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fcy_full_validation.pdf.gz | 626.1 KB | Display | |
Data in XML | 5fcy_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 5fcy_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/5fcy ftp://data.pdbj.org/pub/pdb/validation_reports/fc/5fcy | HTTPS FTP |
-Related structure data
Related structure data | 5fcxC 4xb4S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19183.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria) Strain: PCC 7120 / UTEX 2576 / Gene: all1123 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q8YXT8 |
---|---|
#2: Chemical | ChemComp-BCR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 10% 2-propanol, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.508→32.419 Å / Num. obs: 5403 / % possible obs: 98 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 2.51→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 5.1 / % possible all: 83.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XB4 Resolution: 2.508→32.419 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 30.16 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.508→32.419 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|