[English] 日本語
![](img/lk-miru.gif)
- PDB-1m1p: P21 crystal structure of the tetraheme cytochrome c3 from Shewane... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1m1p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1 | |||||||||
![]() | Small tetraheme cytochrome c | |||||||||
![]() | ELECTRON TRANSPORT / tetraheme cytochrome c | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leys, D. / Meyer, T.E. / Tsapin, A.I. / Nealson, K.H. / Cusanovich, M.A. / Van Beeumen, J.J. | |||||||||
![]() | ![]() Title: Crystal structures at atomic resolution reveal the novel concept of 'electron-harvesting' as a role for the small tetraheme cytochrome c Authors: Leys, D. / Meyer, T.E. / Tsapin, A.I. / Nealson, K.H. / Cusanovich, M.A. / Van Beeumen, J.J. | |||||||||
History |
| |||||||||
Remark 999 | SEQUENCE the sequence of this protein is derived from both N-terminal sequencing and from the ...SEQUENCE the sequence of this protein is derived from both N-terminal sequencing and from the sequenced genome of Shewanella oneidensis strain MR1. The protein sequence is, at present, not available in any protein sequence database. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 166.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
-
Components
#1: Protein | Mass: 9673.621 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEC / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: ammonium sulphate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / PH range low: 9.2 / PH range high: 8.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→15 Å / Num. all: 91758 / Num. obs: 84418 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.55→1.59 Å / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 83876 / Num. measured all: 197538 / Rmerge(I) obs: 0.064 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Identical protein in P212121 spacegroup Resolution: 1.55→14.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.456 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.089 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.014 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→14.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.178 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.55 Å / Lowest resolution: 1.59 Å |