[English] 日本語
![](img/lk-miru.gif)
- PDB-4raz: Crystal structure of Magnetospirillum gryphiswaldense MSR-1 holo-Fur -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4raz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Magnetospirillum gryphiswaldense MSR-1 holo-Fur | ||||||
![]() | DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family) | ||||||
![]() | METAL BINDING PROTEIN / ferric uptake regulator (FUR) / metal ion activation / operator recognition / ![]() | ||||||
Function / homology | ![]() DNA-binding transcription factor activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, Z. / Wang, Q. / Chen, Z. | ||||||
![]() | ![]() Title: Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Authors: Deng, Z. / Wang, Q. / Liu, Z. / Zhang, M. / Machado, A.C. / Chiu, T.P. / Feng, C. / Zhang, Q. / Yu, L. / Qi, L. / Zheng, J. / Wang, X. / Huo, X. / Qi, X. / Li, X. / Wu, W. / Rohs, R. / Li, Y. / Chen, Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4raySC ![]() 4rb0C ![]() 4rb1C ![]() 4rb2C ![]() 4rb3C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16626.541 Da / Num. of mol.: 2 / Mutation: C9L, M14V, M16V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: MSR-1 v2 / Gene: Fur, MGMSRv2_3137 / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.59 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 130 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. all: 36939 / Num. obs: 36732 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible all: 95.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 4RAY Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.926 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.471 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|