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- PDB-1dv3: PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN TH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dv3 | ||||||
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Title | PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-SEPARATED D+QAQB-STATE WITH THE PROTON TRANSFER INHIBITOR CD2+ | ||||||
![]() | (PHOTOSYNTHETIC REACTION CENTER REACTION ...) x 3 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Axelrod, H.L. / Abresch, E.C. / Paddock, M.L. / Okamura, M.Y. / Feher, G. | ||||||
![]() | ![]() 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. #1: ![]() Title: Identification of the Proton Pathway in Bacterial Reaction Centers: Inhibition of Proton Transfer by Binding of Zn2+ or Cd2+ Authors: Paddock, M.L. / Graige, M.S. / Feher, G. / Okamura, M.Y. #2: ![]() 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. #3: ![]() Title: Light-Induced Structural Changes in Photosynthetic Reaction Center: Implications for Mechanism of Electron-Proton Transfer Authors: Stowell, M.H. / McPhillips, T.M. / Rees, D.C. / Soltis, S.M. / Abresch, E. / Feher, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365.5 KB | Display | ![]() |
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PDB format | ![]() | 294.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer composed of chain L, chain M, chain H, and bound cofactors |
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Components
-PHOTOSYNTHETIC REACTION CENTER REACTION ... , 3 types, 6 molecules LRMSHT
#1: Protein | Mass: 31346.389 Da / Num. of mol.: 2 / Fragment: L CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 34355.520 Da / Num. of mol.: 2 / Fragment: M CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 28137.398 Da / Num. of mol.: 2 / Fragment: H CHAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 8 types, 430 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/U10.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LDA.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-BCL / ![]() #5: Chemical | ChemComp-BPH / ![]() #6: Chemical | ChemComp-U10 / ![]() #7: Chemical | #8: Chemical | ![]() #9: Chemical | ![]() #10: Chemical | #11: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.36 % | |||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, heptanetriol, TRIS-HCL, LDAO detergent, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.49→27.8 Å / Num. all: 94618 / Num. obs: 91189 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 49.14 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.49→2.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Num. unique all: 5527 / % possible all: 78.3 |
Reflection | *PLUS Num. obs: 12363 / Num. measured all: 91189 |
Reflection shell | *PLUS % possible obs: 78.3 % |
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Processing
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Refinement | Resolution: 2.5→27.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber Details: Bulk solvent correction applied during the refinement. Refinement was carried out with a maximum likelihood target function and non-crystallographic symmetry restraints.
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Refinement step | Cycle: LAST / Resolution: 2.5→27.8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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