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Yorodumi- PDB-8vtj: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vtj | |||||||||
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Title | Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-cyanophenylalanine | |||||||||
Components | (Reaction center protein ...) x 3 | |||||||||
Keywords | PHOTOSYNTHESIS / membrane protein / electron transfer | |||||||||
Function / homology | Function and homology information plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding Similarity search - Function | |||||||||
Biological species | Cereibacter sphaeroides (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Mathews, I. / Tran, K. / Boxer, S.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-cyanophenylalanine Authors: Mathews, I. / Tran, K. / Boxer, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vtj.cif.gz | 372.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vtj.ent.gz | 298.7 KB | Display | PDB format |
PDBx/mmJSON format | 8vtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vtj_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8vtj_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 8vtj_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 8vtj_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/8vtj ftp://data.pdbj.org/pub/pdb/validation_reports/vt/8vtj | HTTPS FTP |
-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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Unit cell |
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-Components
-Reaction center protein ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: puhA / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y7 |
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#2: Protein | Mass: 31346.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: pufL / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y8 |
#3: Protein | Mass: 33722.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: pufM / Production host: Cereibacter sphaeroides (bacteria) / References: UniProt: P0C0Y9 |
-Non-polymers , 9 types, 125 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | ChemComp-U10 / | #7: Chemical | ChemComp-CL / | #8: Chemical | #9: Chemical | ChemComp-FE / | #10: Chemical | ChemComp-SPO / | #11: Chemical | ChemComp-CDL / | #12: 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: 5.48 Å3/Da / Density % sol: 77.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1 M potassium phosphate, 3.5% 1,2,3-heptanetriol, and 0.1% LDAO precipitant solution; 1.4-1.5 M potassium phosphate reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 250 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97893 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→40 Å / Num. obs: 53054 / % possible obs: 99.8 % / Redundancy: 22.6 % / Biso Wilson estimate: 59.7 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2759 / Rpim(I) all: 0.05918 / Rrim(I) all: 0.281 / Net I/σ(I): 13.01 |
Reflection shell | Resolution: 2.81→2.91 Å / Redundancy: 22.1 % / Rmerge(I) obs: 2.275 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 5188 / CC1/2: 0.69 / CC star: 0.876 / Rpim(I) all: 0.4899 / Rrim(I) all: 2.382 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→39.85 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML
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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: 54.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→39.85 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -45.9308 Å / Origin y: 41.8292 Å / Origin z: 3.2282 Å
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Refinement TLS group | Selection details: all |