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Yorodumi- PDB-8vtl: Crystal structure of R. sphaeroides Photosynthetic Reaction Cente... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vtl | |||||||||
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Title | Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant Y(M210)2-methoxyphenylalanine | |||||||||
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: 3.05 Å | |||||||||
Authors | Tran, K. / Mathews, I. / 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-methoxyphenylalanine Authors: Tran, K. / Mathews, I. / 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 | 8vtl.cif.gz | 371.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vtl.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vtl_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8vtl_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8vtl_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 8vtl_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/8vtl ftp://data.pdbj.org/pub/pdb/validation_reports/vt/8vtl | 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: 26022.904 Da / Num. of mol.: 1 / Fragment: UNP residues 11-250 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: 33727.762 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 , 8 types, 28 molecules
#4: Chemical | #5: Chemical | ChemComp-BCL / #6: Chemical | ChemComp-CL / | #7: Chemical | #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-SPO / | #10: Chemical | ChemComp-CDL / | #11: 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: 5.67 Å3/Da / Density % sol: 78.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop 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: 3.05→39.89 Å / Num. obs: 41821 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 73.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2113 / Rpim(I) all: 0.0653 / Rrim(I) all: 0.216 / Net I/σ(I): 13.35 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.849 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 4111 / CC1/2: 0.667 / CC star: 0.858 / Rpim(I) all: 0.5608 / Rrim(I) all: 1.987 / % possible all: 99.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→39.89 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.21 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→39.89 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: 82.301 Å / Origin y: -18.9894 Å / Origin z: 34.3638 Å
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Refinement TLS group | Selection details: all |