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Yorodumi- PDB-8or7: Structure of a far-red induced allophycocyanin from Chroococcidio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8or7 | ||||||
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Title | Structure of a far-red induced allophycocyanin from Chroococcidiopsis thermalis sp. PCC 7203 | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Phycobiliprotein / Allophycocyanin / Far-red light photoacclimation | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | Chroococcidiopsis thermalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhou, L.J. / Hoeppner, A. / Wang, Y.Q. / Zhao, K.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Photosynth.Res. / Year: 2024 Title: Crystallographic and biochemical analyses of a far-red allophycocyanin to address the mechanism of the super-red-shift. Authors: Zhou, L.J. / Hoppner, A. / Wang, Y.Q. / Hou, J.Y. / Scheer, H. / Zhao, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8or7.cif.gz | 140 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8or7.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 8or7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/8or7 ftp://data.pdbj.org/pub/pdb/validation_reports/or/8or7 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
-Protein , 2 types, 4 molecules BDAC
#1: Protein | Mass: 18553.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_1033 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TVG8 #2: Protein | Mass: 18174.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_1032 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TX42 |
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-Non-polymers , 4 types, 13 molecules
#3: Chemical | ChemComp-CYC / #4: Chemical | ChemComp-K / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-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: 3.57 Å3/Da / Density % sol: 65.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.0 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→77.52 Å / Num. obs: 32743 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 16.9 % / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4760 / CC1/2: 0.843 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→77.52 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.216 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.612 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.646 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→77.52 Å
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Refine LS restraints |
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