[English] 日本語
![](img/lk-miru.gif)
- PDB-6oty: Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectina... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6oty | ||||||
---|---|---|---|---|---|---|---|
Title | Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 4.0 | ||||||
![]() |
| ||||||
![]() | OXYGEN TRANSPORT / hemeprotein | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marchany-Rivera, D. / Smith, C.A. / Rodriguez-Perez, J.D. / Lopez-Garriga, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility. Authors: Marchany-Rivera, D. / Smith, C.A. / Rodriguez-Perez, J.D. / Lopez-Garriga, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 142.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 111.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6otwC ![]() 6otxC ![]() 3pt8S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17146.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
---|---|---|---|
#2: Protein | Mass: 17450.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.75 % |
---|---|
Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 4 / Details: Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.598→50 Å / Num. obs: 13907 / % possible obs: 99.5 % / Redundancy: 7.7 % / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.598→2.64 Å / Num. unique obs: 784334 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3PT8 Resolution: 2.598→33.862 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.98
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.34 Å2 / Biso mean: 77.7341 Å2 / Biso min: 36.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.598→33.862 Å
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 24.2556 Å / Origin y: -27.4411 Å / Origin z: -24.6733 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|