[English] 日本語
![](img/lk-miru.gif)
- PDB-3da3: Crystal Structure of Colicin M, A Novel Phosphatase Specifically ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3da3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Colicin M, A Novel Phosphatase Specifically Imported by Escherichia Coli | ||||||
![]() | Colicin-M | ||||||
![]() | ANTIBIOTIC / Colicin / Phosphatase / Xray / Dimer / three functional domains / Antimicrobial / Bacteriocin / Plasmid / TonB box | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeth, K. / Albrecht, R. / Romer, C. / Braun, V. | ||||||
![]() | ![]() Title: Crystal structure of colicin M, a novel phosphatase specifically imported by Escherichia coli Authors: Zeth, K. / Romer, C. / Patzer, S.I. / Braun, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 113.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 89.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 446.4 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
3 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 2 - 271 / Label seq-ID: 2 - 271
|
-
Components
#1: Protein | Mass: 30412.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.72 % |
---|---|
Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20% PEG 3350, 0.2M potassium nitrate, 0.1mM CaCl2, 0.1mM pyrophosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 282K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 23282 / % possible obs: 93.2 % / Observed criterion σ(I): 2.7 / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3858 / % possible all: 98 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.076 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2067 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
|