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Yorodumi- PDB-1k6n: E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic React... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k6n | ||||||
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Title | E(L212)A,D(L213)A Double Mutant Structure of Photosynthetic Reaction Center from Rhodobacter Sphaeroides | ||||||
Components | (PHOTOSYNTHETIC REACTION CENTER ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / Double Mutant Photosynthetic Reaction Center / proton transfer / 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 / rigid-body refinement / Resolution: 3.1 Å | ||||||
Authors | Pokkuluri, P.R. / Laible, P.D. / Deng, Y.-L. / Wong, T.N. / Hanson, D.K. / Schiffer, M. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The structure of a mutant photosynthetic reaction center shows unexpected changes in main chain orientations and quinone position. Authors: Pokkuluri, P.R. / Laible, P.D. / Deng, Y.L. / Wong, T.N. / Hanson, D.K. / Schiffer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k6n.cif.gz | 204.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k6n.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k6n_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1k6n_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 1k6n_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 1k6n_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k6n ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k6n | HTTPS FTP |
-Related structure data
Related structure data | 1k6lSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-PHOTOSYNTHETIC REACTION CENTER ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31244.346 Da / Num. of mol.: 1 / Mutation: E212A, D213A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: PUFQBALMX / Plasmid: pRKHTL212-213AA / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DeltaDelta11 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 35365.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: PUFQBALMX / Plasmid: pRKHTMHBgl / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DeltaDelta11 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: PUFQBALMX / Plasmid: pRKHTMHBgl / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DeltaDelta11 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 8 types, 144 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-LDA / #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-SPN / | #10: Chemical | ChemComp-CDL / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 5.72 Å3/Da / Density % sol: 78.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: potassium phosphate, ldao, heptane triol, dioxane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 6, 2000 / Details: Mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→15 Å / Num. all: 36275 / Num. obs: 36275 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3316 / % possible all: 84.8 |
Reflection | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 10 Å / Num. obs: 31830 / % possible obs: 92 % / Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS % possible obs: 85 % / Rmerge(I) obs: 0.246 |
-Processing
Software |
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Refinement | Method to determine structure: rigid-body refinement Starting model: 1K6L Resolution: 3.1→10 Å / σ(F): 2 Details: The structure was not refined; model rebuilt to fit the electron density and regularized with the program CHAIN to optimize the geometry
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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Software | *PLUS Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Num. reflection obs: 31830 / Rfactor Rfree: 0.2074 / Rfactor Rwork: 0.203 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |