[English] 日本語
![](img/lk-miru.gif)
- PDB-4m35: Crystal structure of gated-pore mutant H126/141D of second DNA-Bi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4m35 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of gated-pore mutant H126/141D of second DNA-Binding protein under starvation from Mycobacterium smegmatis | ||||||
![]() | Putative starvation-induced DNA protecting protein/Ferritin and Dps | ||||||
![]() | DNA BINDING PROTEIN / ferritin-like fold / DNA binding / ferroxidation / Iron | ||||||
Function / homology | ![]() oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Williams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D. | ||||||
![]() | ![]() Title: A histidine aspartate ionic lock gates the iron passage in miniferritins from Mycobacterium smegmatis Authors: Williams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 139.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 108.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 454.8 KB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m32C ![]() 4m33C ![]() 4m34C ![]() 2z90S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 18466.568 Da / Num. of mol.: 4 / Mutation: H126D, H141D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE2 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 6.5 Details: 50mM MgCl2, 0.1M sodium cacodylate, 20% PEG3350 , pH 6.5, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2011 |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 41264 / Redundancy: 7 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 11.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Direct refinement against model PDB Starting model: 2z90 Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.424 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.356 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.106 Å / Total num. of bins used: 20
|