[English] 日本語
![](img/lk-miru.gif)
- PDB-4dp4: The 1.54 Angstrom crystal structure of reduced (CuI) poplar plast... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4dp4 | ||||||
---|---|---|---|---|---|---|---|
Title | The 1.54 Angstrom crystal structure of reduced (CuI) poplar plastocyanin B at pH 6.0 | ||||||
![]() | Plastocyanin B, chloroplastic | ||||||
![]() | ELECTRON TRANSPORT / membrane / thylakoid / transit peptide / plastocyanin-like domain / copper-binding | ||||||
Function / homology | ![]() electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kachalova, G.S. / Shosheva, A.H. / Bourenkov, G.P. / Donchev, A.A. / Dimitrov, M.I. / Bartunik, H.D. | ||||||
![]() | ![]() Title: Structural comparison of the poplar plastocyanin isoforms PCa and PCb sheds new light on the role of the copper site geometry in interactions with redox partners in oxygenic photosynthesis. Authors: Kachalova, G.S. / Shosheva, A.C. / Bourenkov, G.P. / Donchev, A.A. / Dimitrov, M.I. / Bartunik, H.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 36.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 24.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dp0C ![]() 4dp1C ![]() 4dp2C ![]() 4dp5C ![]() 4dp6C ![]() 4dp7C ![]() 4dp8C ![]() 4dp9C ![]() 4dpaC ![]() 4dpbC ![]() 4dpcC ![]() 1plcS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10474.645 Da / Num. of mol.: 1 / Fragment: UNP residues 70-168 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CU1 / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.67 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.6 M ammonium sulfate, 0.1 M sodium acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2002 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→14.74 Å / Num. all: 11813 / Num. obs: 11778 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 15.01 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.2 / Num. unique all: 584 / % possible all: 98.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PLC Resolution: 1.54→14.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.833 / SU ML: 0.063 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→14.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.54→1.578 Å / Total num. of bins used: 20
|