[English] 日本語
![](img/lk-miru.gif)
- PDB-3mz2: Crystal structure of a Glycerophosphoryl diester phosphodiesteras... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3mz2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution | ||||||
![]() | Glycerophosphoryl diester phosphodiesterase![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 256.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 33783.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 552 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-PG4 / ![]() #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-PE4 / | ![]() #6: Water | ChemComp-HOH / | ![]() |
---|
-Details
Sequence details | THIS CONSTRUCT (RESIDUES 26-316) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 26-316) WAS EXPRESSED WITH A PURIFICATI |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.77 % |
---|---|
Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 27.0000% polyethylene glycol 4000, 0.3000M ammonium sulfate, 0.1M sodium acetate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→47.615 Å / Num. obs: 77355 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.681 Å2 / Rsym value: 0.08 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing![]() | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF NA IONS. 6. SODIUM (NA), SULPHATE (SO4) IONS, A PEG-4000 (PE4) FRAGMENT AND PEG-200 (PG4) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.26 Å2 / Biso mean: 19.3 Å2 / Biso min: 5.19 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→47.615 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|