[English] 日本語
![](img/lk-miru.gif)
- PDB-1rzh: PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPH... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1rzh | ||||||
---|---|---|---|---|---|---|---|
Title | PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-NEUTRAL DQAQB STATE (TRIGONAL FORM) | ||||||
![]() | (Reaction center protein ...![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, Q. / Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. | ||||||
![]() | ![]() 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. #1: ![]() Title: Characterization of Second Site Mutations Show that Fast Proton Transfer to Qb- is Restored in Bacterial Reaction Centers of Rhodobacter Sphaeroides Containing the Asp-L213->Asn Lesion Authors: Paddock, M.L. / Senft, M.E. / Graige, M.S. / Rongey, S.H. / Turanchik, T. / Feher, G. / Okamura, M.Y. #2: ![]() Title: Determination of the Binding Sites of the Proton Transfer Inhibitors Cd2+ and Zn2+ in Bacterial Reaction Centers Authors: Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. #3: ![]() Title: Identification of Proton Transfer Pathways in the X-Ray Crystal Structure of the Bacterial Reaction Center from Rhodobacter Sphaeroides Authors: Abresch, E.C. / Paddock, M.L. / Stowell, M.H.B. / McPhillips, T.M. / Axelrod, H.L. / Soltis, S.M. / Rees, D.C. / Okamura, M.Y. / Feher, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 212 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 161.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1rvjC ![]() 1ry5C ![]() 1rzzC ![]() 1s00C ![]() 1qovS C: citing same article ( 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: 31345.404 Da / Num. of mol.: 1 / Mutation: D213N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | ![]() Mass: 34344.488 Da / Num. of mol.: 1 / Mutation: R233C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 11 types, 489 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/HTO.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/SPO.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / ![]() #5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | #8: Chemical | ChemComp-FE2 / | #9: Chemical | ChemComp-PO4 / | ![]() #10: Chemical | ChemComp-SPO / | #11: Chemical | ![]() #12: Chemical | ChemComp-CDL / | ![]() #13: Chemical | ChemComp-GOL / | ![]() #14: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.2 Å3/Da / Density % sol: 76 % |
---|---|
Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: potassium phosphate, sodium chloride, LDAO, haptanetriol, haxanetriol, dioxane, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→39.31 Å / Num. all: 188308 / Num. obs: 188308 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.098 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.344 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1QOV Resolution: 1.8→39.31 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2694188.38 / 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: 52.6307 Å2 / ksol: 0.355853 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
|