[English] 日本語
![](img/lk-miru.gif)
- PDB-2ux5: X-ray high resolution structure of the photosynthetic reaction ce... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ux5 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 9 in the charge-separated state | ||||||
![]() | (REACTION CENTER PROTEIN ...) x 3 | ||||||
![]() | PHOTOSYNTHESIS / BACTERIOCHLOROPHYLL / PHOSPHATIDYLCHOLINE / CHLOROPHYLL / CARDIOLIPIN / METAL-BINDING / TRANSMEMBRANE / GLUCOSYLGALACTOSYL DIACYLGLYCEROL / PROTON TRANSLOCATION PATHWAYS / REACTION CENTER / ELECTRON TRANSPORT / IRON / MEMBRANE / TRANSPORT / MAGNESIUM / CHROMOPHORE / BINDING POSITIONS OF THE SECONDARY QUINONE QB | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koepke, J. / Diehm, R. / Fritzsch, G. | ||||||
![]() | ![]() Title: Ph Modulates the Quinone Position in the Photosynthetic Reaction Center from Rhodobacter Sphaeroides in the Neutral and Charge Separated States. Authors: Koepke, J. / Krammer, E.M. / Klingen, A.R. / Sebban, P. / Ullmann, G.M. / Fritzsch, G. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 218 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 168.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 64.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j8cC ![]() 2j8dC ![]() 2uwsC ![]() 2uwtC ![]() 2uwuC ![]() 2uwvC ![]() 2uwwC ![]() 2ux3C ![]() 2ux4C ![]() 2uxjC ![]() 2uxkC ![]() 2uxlC ![]() 2uxmC ![]() 1pcrS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-REACTION CENTER PROTEIN ... , 3 types, 3 molecules HLM
#1: Protein | Mass: 28066.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 6.5 CHARGE-SEPARATED STATE / Source: (natural) ![]() |
---|---|
#2: Protein | Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 6.5 CHARGE-SEPARATED STATE / Source: (natural) ![]() |
#3: Protein | Mass: 34398.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 6.5 CHARGE-SEPARATED STATE / Source: (natural) ![]() |
-Non-polymers , 12 types, 435 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/UQ2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCL.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/UQ2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-BCL / #6: Chemical | ChemComp-LDA / #7: Chemical | #8: Chemical | ChemComp-UQ2 / | #9: Chemical | ChemComp-PO4 / | #10: Chemical | ChemComp-HTO / | #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-U10 / | #13: Chemical | ChemComp-SPO / | #14: Chemical | ChemComp-CDL / | #15: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.81 Å3/Da / Density % sol: 74.21 % / Description: NONE |
---|---|
Crystal grow | pH: 9 / Details: pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 14, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8457 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 103587 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.29 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.72 / % possible all: 89.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PCR Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.042 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5 RESIDUES OF THE M SUBUNIT C-TERM ARE MISSING, 10 RESIDUES EACH OF THE H SUBUNIT C- AND N-TERM ARE MISSING
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|