[English] 日本語
![](img/lk-miru.gif)
- PDB-4ero: Study on structure and function relationships in human Pirin with... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ero | ||||||
---|---|---|---|---|---|---|---|
Title | Study on structure and function relationships in human Pirin with Cobalt ion | ||||||
![]() | Pirin | ||||||
![]() | OXIDOREDUCTASE / beta sandwich / cupin / metatl binding protein / transcription activity / protein binding / nucleus | ||||||
Function / homology | ![]() Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / nucleus ...Digestion / quercetin 2,3-dioxygenase / quercetin 2,3-dioxygenase activity / monocyte differentiation / digestion / transcription coregulator activity / transcription by RNA polymerase II / nuclear body / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Liu, F. / Rehmani, I. / Fu, R. / Esaka, S. / Chen, L. / Serrano, V. / Liu, A. | ||||||
![]() | ![]() Title: Pirin is an iron-dependent redox regulator of NF-kappa B. Authors: Liu, F. / Rehmani, I. / Esaki, S. / Fu, R. / Chen, L. / de Serrano, V. / Liu, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4ewaC ![]() 4ewdC ![]() 4eweC ![]() 4gulC ![]() 4hltC ![]() 4ewb C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 32159.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-CO / | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.58 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 200000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 11040 / Num. obs: 9285 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.6 / Num. unique all: 345 / % possible all: 66 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.65→25.08 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 0.68 / SU B: 7.88 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 58.79 Å2 / Biso mean: 14.6705 Å2 / Biso min: 2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→25.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.65→2.718 Å / Total num. of bins used: 20
|