[English] 日本語
![](img/lk-miru.gif)
- PDB-5g3p: Bacillus cereus formamidase (BceAmiF) acetylated at the active site. -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5g3p | ||||||
---|---|---|---|---|---|---|---|
Title | Bacillus cereus formamidase (BceAmiF) acetylated at the active site. | ||||||
![]() | FORMAMIDASE | ||||||
![]() | HYDROLASE / FORMAMIDASE / AMIDASE / NITRILASE SUPERFAMILY | ||||||
Function / homology | ![]() formamidase / formamidase activity / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / : Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gavira, J.A. / Conejero-Muriel, M. / Martinez-Rodriguez, S. | ||||||
![]() | ![]() Title: A novel cysteine carbamoyl-switch is responsible for the inhibition of formamidase, a nitrilase superfamily member. Authors: Martinez-Rodriguez, S. / Conejero-Muriel, M. / Gavira, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 435.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 356.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 553.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 571.3 KB | Display | |
Data in XML | ![]() | 93 KB | Display | |
Data in CIF | ![]() | 135.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g3oC ![]() 2dyuS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 38715.762 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: ACETYLATED AT CYSTEINE 165 IN ALL THE CHAINS. / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 8 types, 1981 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-PGE / #7: Chemical | ChemComp-PG4 / | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % / Description: NONE |
---|---|
Crystal grow | Method: counter-diffusion / pH: 4 Details: CAPILLARY COUNTER DIFFUSION 20% PEG 400, 15% PEG 4K, 10% PEG 8K, NAAC 0.1M PH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→28.38 Å / Num. obs: 182788 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.26 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.73 / % possible all: 63 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DYU Resolution: 1.78→103.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.981 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→103.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|