[English] 日本語
![](img/lk-miru.gif)
- PDB-3r0g: 3D Structure of Ferric Methanosarcina Acetivorans Protoglobin I14... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3r0g | ||||||
---|---|---|---|---|---|---|---|
Title | 3D Structure of Ferric Methanosarcina Acetivorans Protoglobin I149F mutant in Aquomet form | ||||||
![]() | Methanosarcina acetivorans protoglobin | ||||||
![]() | OXYGEN BINDING / OXYGEN TRANSPORT / protoglobin / globin fold / METHANOGENESIS / ARCHAEA PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pesce, A. / Tilleman, L. / Dewilde, S. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Bruno, S. / Moens, L. / Bolognesi, M. / Nardini, M. | ||||||
![]() | ![]() Title: Structural heterogeneity and ligand gating in ferric methanosarcina acetivorans protoglobin mutants. Authors: Pesce, A. / Tilleman, L. / Dewilde, S. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Bruno, S. / Moens, L. / Bolognesi, M. / Nardini, M. #1: ![]() Title: Archaeal protoglobin structure indicates new ligand diffusion paths and modulation of haem-reactivity Authors: Nardini, M. / Pesce, A. / Thijs, L. / Saito, J.A. / Dewilde, S. / Alam, M. / Ascenzi, P. / Coletta, M. / Ciaccio, C. / Moens, L. / Bolognesi, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qzxC ![]() 3qzzC ![]() 2vebS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23044.879 Da / Num. of mol.: 2 / Mutation: C101S, I149F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 176 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IPA / | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.54 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 10% isopropanol, 20% PEG 4000, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→78.81 Å / Num. obs: 19625 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2VEB Resolution: 2.2→49.64 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 9.275 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE HEPES MOLECULE IS PARTLY DISORDERED, AS INDICATED BY HIGH B-FACTORS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.777 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
|