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Yorodumi- PDB-8qx7: Apo-C-Terminal Domain Homolog of the Orange Carotenoid Protein fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qx7 | ||||||
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Title | Apo-C-Terminal Domain Homolog of the Orange Carotenoid Protein from Anabaena at a resolution of 1.95 Angstroms | ||||||
Components | All4940 protein | ||||||
Keywords | PHOTOSYNTHESIS / Membrane / carotenoid / Orange carotenoid protein / Cyanobacteria | ||||||
Function / homology | Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily / MALONIC ACID / All4940 protein Function and homology information | ||||||
Biological species | Cyanobacteriota (blue-green algae) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Sklyar, J. / Wilson, A. / Kirilovsky, D. / Adir, N. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Insights into energy quenching mechanisms and carotenoid uptake by orange carotenoid protein homologs: HCP4 and CTDH. Authors: Sklyar, J. / Wilson, A. / Kirilovsky, D. / Adir, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qx7.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qx7.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 8qx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qx7_validation.pdf.gz | 958.4 KB | Display | wwPDB validaton report |
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Full document | 8qx7_full_validation.pdf.gz | 962 KB | Display | |
Data in XML | 8qx7_validation.xml.gz | 13 KB | Display | |
Data in CIF | 8qx7_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/8qx7 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/8qx7 | HTTPS FTP |
-Related structure data
Related structure data | 8qx5C 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
#1: Protein | Mass: 16158.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanobacteriota (blue-green algae) / Gene: all4940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YMJ3 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 44% Tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.78 Å / Num. obs: 20695 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 1410 / CC1/2: 0.843 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 26.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→47.78 Å
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Refine LS restraints |
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LS refinement shell |
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