[English] 日本語
![](img/lk-miru.gif)
- PDB-3dr4: GDP-perosamine synthase K186A mutant from Caulobacter crescentus ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dr4 | ||||||
---|---|---|---|---|---|---|---|
Title | GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand | ||||||
![]() | Putative perosamine synthetase | ||||||
![]() | TRANSFERASE / Perosamine / deoxysugar / pyridoxal phosphate / aspartate aminotransferase / o-antigen | ||||||
Function / homology | ![]() GDP-perosamine synthase / GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity / O antigen biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Holden, H.M. / Cook, P.D. / Carney, A.E. | ||||||
![]() | ![]() Title: Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase Authors: Cook, P.D. / Carney, A.E. / Holden, H.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 326.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 259.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 70.9 KB | Display | |
Data in CIF | ![]() | 101.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dr7C ![]() 3bn1S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42980.969 Da / Num. of mol.: 4 / Mutation: K186A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-G4M / [( #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch / pH: 6.5 Details: 50 mM MES, 10% PEG 8000, 1 mM PLP, 1mM glutamate, pH 6.5, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Feb 8, 2008 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 202983 / Num. obs: 186452 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.041 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 16930 / Rsym value: 0.214 / % possible all: 83.8 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3bn1 Resolution: 1.6→26.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→26.2 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|