[English] 日本語
![](img/lk-miru.gif)
- PDB-3gkm: Insights into the Alkyl Peroxide Reduction Activity of Xanthomona... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gkm | ||||||
---|---|---|---|---|---|---|---|
Title | Insights into the Alkyl Peroxide Reduction Activity of Xanthomonas campestris Bacterioferritin Comigratory Protein from the Trapped Intermediate/Ligand Complex Structures | ||||||
![]() | Bacterioferritin comigratory protein | ||||||
![]() | OXIDOREDUCTASE / Xanthomonas campestris / Bcp / Prx / Atypical 2-Cys | ||||||
Function / homology | ![]() thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Liao, S.-J. | ||||||
![]() | ![]() Title: Insights into the alkyl peroxide reduction pathway of Xanthomonas campestris bacterioferritin comigratory protein from the trapped intermediate-ligand complex structures Authors: Liao, S.-J. / Yang, C.-Y. / Chin, K.-H. / Wang, A.H.-J. / Chou, S.-H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441.4 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gkkSC ![]() 3gknC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17539.896 Da / Num. of mol.: 1 / Mutation: C48S, C84S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 17 / Gene: BCP / Plasmid: pET / Production host: ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-FMT / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.88 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 5.5 Details: 36% PEG 4000, 0.1M cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→30 Å / Num. obs: 20772 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 37.908 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 10.836 / Rsym value: 0.127 / % possible all: 96.6 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GKK Resolution: 1.53→23.25 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.44 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→23.25 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.53→1.58 Å / % reflection Rfree: 5 % / % reflection obs: 96.6 % | ||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein_rep.top |