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Yorodumi- PDB-1rqk: Structure of the reaction centre from Rhodobacter sphaeroides car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rqk | ||||||
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Title | Structure of the reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1 reconstituted with 3,4-dihydrospheroidene | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Roszak, A.W. / Hashimoto, H. / Gardiner, A.T. / 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 | 1rqk.cif.gz | 208.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rqk.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rqk_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 1rqk_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 1rqk_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 1rqk_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/1rqk ftp://data.pdbj.org/pub/pdb/validation_reports/rq/1rqk | 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 3,4-dihydrospheroidene, also known as methoxyneurosporene. 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, 226 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-LDA / #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-SP2 / | #10: Chemical | ChemComp-CDL / | #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 grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Trisodium citrate, LDAO, 1,2,3-heptanetriol, Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 16.0K |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Dec 20, 2001 / Details: MacScience mirrors |
Radiation | Monochromator: MacScience mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15.285 Å / Num. all: 57635 / Num. obs: 57635 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2800 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→15.285 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 16.734 / SU ML: 0.145 / 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: 0.249 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 AND CDL 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: 47.644 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15.285 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.2231 Å / Origin y: 103.7725 Å / Origin z: 34.2874 Å
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Refinement TLS group |
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