+
Open data
-
Basic information
Entry | Database: PDB / ID: 3a6f | ||||||
---|---|---|---|---|---|---|---|
Title | W174F mutant creatininase, Type II | ||||||
![]() | Creatinine amidohydrolase | ||||||
![]() | HYDROLASE / creatinine amidohydrolase / urease-related amidohydrolase superfamily | ||||||
Function / homology | ![]() creatininase / creatininase activity / creatinine catabolic process / creatine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / riboflavin biosynthetic process / manganese ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakajima, Y. / Yamashita, K. / Ito, K. / Yoshimoto, T. | ||||||
![]() | ![]() Title: Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase Authors: Yamashita, K. / Nakajima, Y. / Matsushita, H. / Nishiya, Y. / Yamazawa, R. / Wu, Y.F. / Matsubara, F. / Oyama, H. / Ito, K. / Yoshimoto, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 315.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 256.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 513.4 KB | Display | |
Data in XML | ![]() | 61.7 KB | Display | |
Data in CIF | ![]() | 86.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a6dC ![]() 3a6eC ![]() 3a6gC ![]() 3a6hC ![]() 3a6jC ![]() 3a6kC ![]() 3a6lC ![]() 1j2tS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28559.754 Da / Num. of mol.: 6 / Mutation: W174F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CAC / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 66.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 45% PEG200, 20mM Magnesium chloride, 100mM Sodium cacodylate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2006 / Details: Rhodium coated silicon single crystal |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 242993 / Num. obs: 242993 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 41.8 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 10 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.6 / Num. unique all: 24075 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1J2T Resolution: 1.78→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The diffraction data was detwined with twin fraction of 0.463
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.78→1.84 Å
|