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Yorodumi- PDB-1rgn: Structure of the reaction centre from Rhodobacter sphaeroides car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rgn | ||||||
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Title | Structure of the reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1 reconstituted with spheroidene | ||||||
Components | (Reaction center protein ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / RECONSTITUTED CAROTENOID / CAROTENOID BINDING SITE / MEMBRANE PROTEIN | ||||||
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 / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Roszak, A.W. / Frank, H.A. / McKendrick, K. / Mitchell, I.A. / Cogdell, R.J. / Isaacs, N.W. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Protein Regulation of Carotenoid Binding: Gatekeeper and Locking Amino Acid Residues in Reaction Centers of Rhodobacter sphaeroides Authors: Roszak, A.W. / McKendrick, K. / Gardiner, A.T. / Mitchell, I.A. / Isaacs, N.W. / Cogdell, R.J. / Hashimoto, H. / Frank, H.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rgn.cif.gz | 200.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rgn.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rgn_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 1rgn_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 1rgn_validation.xml.gz | 41 KB | Display | |
Data in CIF | 1rgn_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/1rgn ftp://data.pdbj.org/pub/pdb/validation_reports/rg/1rgn | HTTPS FTP |
-Related structure data
-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 LMH
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26. ...Details: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid.IN THIS ENTRY R-26.1 HAS BEEN RECONSTITUTED WITH CAROTENOID SPHEROIDENE. Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R-26.1 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 8 types, 190 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-LDA / #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-PO4 / | #10: Chemical | ChemComp-SPO / | #11: Water | ChemComp-HOH / | |
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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: 5.54 Å3/Da / Density % sol: 77.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Trisodium citrate, LDAO, 1,2,3-heptanetriol, ethylene glycol, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 14, 1999 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→24 Å / Num. all: 46063 / Num. obs: 46063 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 79.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2377 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 19.4 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: TLS thermal mode followed by the restrained refinement of atomic coordinates and isotropic B-factors; all details in the pdb-file. Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.403 / ESU R Free: 0.284 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron density quality some atoms at the end of the carbohydrate tails of ligands U10 were not modelled
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.611 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.973 Å / Origin y: 102.5517 Å / Origin z: 33.5605 Å
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Refinement TLS group |
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