[English] 日本語
![](img/lk-miru.gif)
- PDB-1jaf: CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS A... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jaf | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT 2.5 ANGSTOMS RESOLUTION | ||||||
![]() | CYTOCHROME C' | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Archer, M. / Banci, L. / Dikaya, E. / Romao, M.J. | ||||||
![]() | Journal: J.Biol.Inorg.Chem. / Year: 1997 Title: Crystal Structure of Cytochrome C' from Rhodocyclus Gelatinosus and Comparison with Other Cytochromes C' Authors: Archer, M. / Banci, L. / Dikaya, E. / Romao, M.J. #1: ![]() Title: One-and Two-Dimensional NMR Characterization of Oxidized and Reduced Cytochrome C' from Rhodocyclus Gelatinosus Authors: Bertini, I. / Gori, G. / Luchinat, C. / Vila, A.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1cgoS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13303.056 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | pH: 6 Details: 55% SATURATED (NH4)2SO4, 50 MM (NH4)2HPO4, 1 M NACL, pH 6. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Type: BRUKER NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→27.4 Å / Num. obs: 13010 / % possible obs: 99.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 96234 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 98.7 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: CYTOCHROME C' FROM ALCALIGENES SP (PDB ENTRY 1CGO) Resolution: 2.5→27.4 Å / Cross valid method: FREE R / σ(F): 2 Details: BULK SOLVENT CORRECTION USED (KSOL=0.33, SOLRAD=0.25 A, B=50 A**2).
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→27.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|