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Yorodumi- PDB-7qd0: Structure of the orange carotenoid protein from Planktothrix agar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qd0 | |||||||||||||||
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Title | Structure of the orange carotenoid protein from Planktothrix agardhii binding echinenone in the C2 space group | |||||||||||||||
Components | Orange carotenoid-binding protein | |||||||||||||||
Keywords | PHOTOSYNTHESIS / CAROTENOID-BINDING / PHOTOPROTECTION / CAROTENOID BINDING PROTEIN | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Planktothrix agardhii (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||||||||
Authors | Andreeva, E.A. / Hartmann, E. / Schlichting, I. / Colletier, J.-P. | |||||||||||||||
Funding support | France, 4items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2022 Title: Structure-function-dynamics relationships in the peculiar Planktothrix PCC7805 OCP1: Impact of his-tagging and carotenoid type. Authors: Wilson, A. / Andreeva, E.A. / Nizinski, S.J. / Talbot, L. / Hartmann, E. / Schlichting, I. / Burdzinski, G. / Sliwa, M. / Kirilovsky, D. / Colletier, J.P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qd0.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qd0.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qd0_validation.pdf.gz | 671.1 KB | Display | wwPDB validaton report |
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Full document | 7qd0_full_validation.pdf.gz | 678.4 KB | Display | |
Data in XML | 7qd0_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 7qd0_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/7qd0 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/7qd0 | HTTPS FTP |
-Related structure data
Related structure data | 7qczC 7qd1C 7qd2C 3mg1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35352.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planktothrix agardhii (bacteria) / Gene: PLAM_2315 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1J1JHR9 |
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-Non-polymers , 5 types, 268 molecules
#2: Chemical | ChemComp-ARG / | ||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-ECH / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium acetate, pH 5 and 10-20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→32.44 Å / Num. obs: 30918 / % possible obs: 98.61 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 13.78 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7233 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 3107 / CC1/2: 0.843 / Rpim(I) all: 0.3882 / Rrim(I) all: 0.7233 / % possible all: 99.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mg1 Resolution: 1.7→32.44 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2509 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→32.44 Å
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Refine LS restraints |
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LS refinement shell |
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