[English] 日本語
![](img/lk-miru.gif)
- PDB-2w8c: Plastocyanin variant with N-terminal Methionine - closed structure -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2w8c | ||||||
---|---|---|---|---|---|---|---|
Title | Plastocyanin variant with N-terminal Methionine - closed structure | ||||||
![]() | PLASTOCYANIN | ||||||
![]() | ELECTRON TRANSPORT / PROTEIN INTERACTIONS / TRANSPORT / CUPREDOXIN / SELF-ASSEMBLY / METAL-BINDING | ||||||
Function / homology | ![]() electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / plasma membrane-derived thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Crowley, P.B. / Matias, P.M. / Khan, A.R. | ||||||
![]() | ![]() Title: Metal-Mediated Self-Assembly of a Beta-Sandwich Protein. Authors: Crowley, P.B. / Matias, P.M. / Khan, A.R. / Roessle, M. / Svergun, D.I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 423.2 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w88SC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
3 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 0 - 105 / Label seq-ID: 1 - 106
NCS oper: (Code: given Matrix: (-0.99189, 0.12694, 0.00654), Vector: |
-
Components
#1: Protein | Mass: 11562.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | NO SIGNAL PEPTIDE PRESENT AND N-TERMINAL MET INSERTION | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE |
---|---|
Crystal grow | Details: 5% PEG 8K, 0.1M ZINC ACETATE, 0.2 M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.9 Å / Num. obs: 20932 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 17.71 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.7 / % possible all: 93.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W88 CHAIN A Resolution: 1.8→65.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.764 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUALS ONLY. RESIDUES VAL 32 A, MET 65 A, SER 78 A, ARG 93 A, MET 65 B AND ARG 93 B WERE MODELLED WITH TWO ALTERNATIVE SIDE-CHAIN CONFORMATIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→65.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|