[English] 日本語
![](img/lk-miru.gif)
- PDB-1czp: ANABAENA PCC7119 [2FE-2S] FERREDOXIN IN THE REDUCED AND OXIXIZED ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1czp | ||||||
---|---|---|---|---|---|---|---|
Title | ANABAENA PCC7119 [2FE-2S] FERREDOXIN IN THE REDUCED AND OXIXIZED STATE AT 1.17 A | ||||||
![]() | FERREDOXIN I | ||||||
![]() | ELECTRON TRANSPORT / [2FE-2S] PROTEIN / CRYSTAL REDUCED WITH DITHIONITE | ||||||
Function / homology | ![]() electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morales, R. / Charon, M.H. / Frey, M. | ||||||
![]() | ![]() Title: Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes. Authors: Morales, R. / Charon, M.H. / Hudry-Clergeon, G. / Petillot, Y. / Norager, S. / Medina, M. / Frey, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 99.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1qt9C ![]() 1fxaS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10705.624 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: 2 Å3/Da / Density % sol: 48.32 % Description: REDUCED CRYSTAL WITH SODIUM DITHIONITE IN ANAEROBIC ATMOSPHERE | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 MM SODIUM SUCCINATE PH 5.5, 2.6 M AMMONIUM SULFATE, 1% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→30 Å / Num. all: 67690 / Num. obs: 67690 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.17→1.22 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 6.1 / % possible all: 89.3 |
Reflection | *PLUS Num. obs: 67611 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 89.3 % |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FXA Resolution: 1.17→15 Å / Num. parameters: 1756 / Num. restraintsaints: 2142 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 StereochEM target val spec case: [2FE-2S] CLUSTERS NOT RESTRAINED Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56. ANISOTROPIC REFINEMENT REDUCED R-FREE (NO CUTOFF) BY 4 %
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1878 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→15 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|