[English] 日本語
![](img/lk-miru.gif)
- PDB-4jxc: X-ray snapshots of possible intermediates in the time course of s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4jxc | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters | ||||||
![]() | FEFE-HYDROGENASE MATURASE | ||||||
![]() | OXIDOREDUCTASE / Radical SAM Protein / FeFe-hydrogenase active site Assembly / Fe4S4 cluster / S-adenosyl-L-methionine | ||||||
Function / homology | ![]() water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / : / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity ...water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / : / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nicolet, Y. / Rohac, R. / Martin, L. / Fontecilla-Camps, J.C. | ||||||
![]() | ![]() Title: X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters. Authors: Nicolet, Y. / Rohac, R. / Martin, L. / Fontecilla-Camps, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 181.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 140.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jy8C ![]() 4jy9C ![]() 4jydC ![]() 4jyeC ![]() 4jyfC ![]() 3ciwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39873.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 10 types, 343 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/1N7.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/1N7.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-SAM / | ||||||||||||||
#4: Chemical | ChemComp-1N7 / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-FES / | #7: Chemical | #8: Chemical | ChemComp-IPA / | #9: Chemical | #10: Chemical | ChemComp-SO4 / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, 200 mM Li2SO4, 30% PEG 4000, Anaerobic chamber (N2/H2 95/5%) , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2005 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→60 Å / Num. all: 119182 / Num. obs: 101819 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.45→1.54 Å / % possible all: 88.06 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3CIW Resolution: 1.5→58.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.316 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 10.767 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→58.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
|