[English] 日本語
Yorodumi- PDB-1yf6: Structure of a quintuple mutant of photosynthetic reaction center... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yf6 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a quintuple mutant of photosynthetic reaction center from rhodobacter sphaeroides | ||||||
Components | (Reaction center protein ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / BACTERIAL PHOTOSYNTHESIS / RHODOBACTER SPHAEROIDES / GATED ELECTRON TRANSFER / QUINONE MOVEMENT / INTEGRAL 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: 2.25 Å | ||||||
Authors | Paddock, M.L. / Chang, C. / Xu, Q. / Abresch, E.C. / Axelrod, H.L. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Quinone (Q(B)) Reduction by B-Branch Electron Transfer in Mutant Bacterial Reaction Centers from Rhodobacter sphaeroides: Quantum Efficiency and X-ray Structure. Authors: Paddock, M.L. / Chang, C. / Xu, Q. / Abresch, E.C. / Axelrod, H.L. / Feher, G. / Okamura, M.Y. #1: Journal: Structure / Year: 2004 Title: X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. Sphaeroides; Altered Proton Transfer Pathways Authors: Xu, Q. / Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yf6.cif.gz | 208.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yf6.ent.gz | 158 KB | Display | PDB format |
PDBx/mmJSON format | 1yf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yf6_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1yf6_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 1yf6_validation.xml.gz | 44 KB | Display | |
Data in CIF | 1yf6_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yf6 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yf6 | HTTPS FTP |
-Related structure data
Related structure data | 1rzhS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Reaction center protein ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31362.389 Da / Num. of mol.: 1 / Mutation: L181Y Source method: isolated from a genetically manipulated source Details: L181Y / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
---|---|
#2: Protein | Mass: 34580.699 Da / Num. of mol.: 1 / Mutation: M203D, M210F, M214H, M260W Source method: isolated from a genetically manipulated source Details: M203D, M210F, M214H, M260W / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Production host: Rhodobacter sphaeroides (bacteria) / 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: puhA / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 12 types, 384 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | ChemComp-BPH / | #6: Chemical | #7: Chemical | ChemComp-HTO / | #8: Chemical | #9: Chemical | ChemComp-GOL / | #10: Chemical | ChemComp-FE2 / | #11: Chemical | ChemComp-CL / | #12: Chemical | #13: Chemical | ChemComp-SPO / | #14: Chemical | ChemComp-CDL / | #15: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.25 Å3/Da / Density % sol: 76.4 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: POTASSIUM PHOSPHATE, SODIUM CHLORIDE, HAPTANETRIOL, DIOXANE, HAXANETRIOL, LDAO, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.34 Å / Num. all: 84130 / Num. obs: 84139 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.091 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.393 / % possible all: 70.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RZH Resolution: 2.25→39.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2952289.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.8034 Å2 / ksol: 0.337419 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→39.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
|