+
Open data
-
Basic information
Entry | Database: PDB / ID: 9iqw | ||||||
---|---|---|---|---|---|---|---|
Title | phage HY126 encoded D-arabinose 1,5-diphosphate phosphatase AfhF | ||||||
![]() | Capsule biosynthesis protein | ||||||
![]() | VIRAL PROTEIN / homotetramer | ||||||
Function / homology | HAD superfamily / HAD-like superfamily / Capsule biosynthesis protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, H. / Lianrong, W. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: structure of bisphosphate phosphatase at 1.64 angstroms resolution Authors: Yu, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 35.9 KB | Display | |
Data in CIF | ![]() | 50.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15405.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.06 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M Mg(HCOO)2.2H2O 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→57.84 Å / Num. obs: 74649 / % possible obs: 99.1 % / Redundancy: 11 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.64→1.68 Å / Rmerge(I) obs: 0.868 / Num. unique obs: 4996 / CC1/2: 0.648 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→57.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|