[English] 日本語
Yorodumi- PDB-7qcz: Structure of the orange carotenoid protein from Planktothrix agar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qcz | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||||||||
Authors | Andreeva, E.A. / Hartmann, E. / Schlichting, I. / Colletier, J.-P. | |||||||||||||||
Funding support | France, 4items
| |||||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qcz.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qcz.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qcz_validation.pdf.gz | 643.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qcz_full_validation.pdf.gz | 650.6 KB | Display | |
Data in XML | 7qcz_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 7qcz_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/7qcz ftp://data.pdbj.org/pub/pdb/validation_reports/qc/7qcz | HTTPS FTP |
-Related structure data
Related structure data | 7qd0C 7qd1C 7qd2C 3mg1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#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 |
---|---|
#2: Chemical | ChemComp-45D / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.64 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M Bis-Tris pH 5.5, 20%-25% PEG 3550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→19.23 Å / Num. obs: 23806 / % possible obs: 92.94 % / Redundancy: 2.4 % / Biso Wilson estimate: 26.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.04 / Rrim(I) all: 0.066 / Net I/σ(I): 11.96 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.5813 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2022 / CC1/2: 0.675 / Rpim(I) all: 0.4513 / Rrim(I) all: 0.7392 / % possible all: 79.92 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mg1 Resolution: 1.85→18.26 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5786 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→18.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|