[English] 日本語
![](img/lk-miru.gif)
- PDB-1a5o: K217C VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1a5o | ||||||
---|---|---|---|---|---|---|---|
Title | K217C VARIANT OF KLEBSIELLA AEROGENES UREASE, CHEMICALLY RESCUED BY FORMATE AND NICKEL | ||||||
![]() |
| ||||||
![]() | HYDROLASE / HYDROLASE (UREA AMIDO) / MUTANT / NICKEL METALLOENZYME | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Pearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P. | ||||||
![]() | ![]() Title: Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand. Authors: Pearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P. #1: ![]() Title: 70 Years of Crystalline Urease: What Have We Learned? Authors: Karplus, P.A. / Pearson, M.A. / Hausinger, R.P. #2: ![]() Title: The Crystal Structure of Urease from Klebsiella Aerogenes Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 158.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 123.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 448.3 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: K217C, C319A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 11125.690 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 60209.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 177 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM HEPES, PH 7.5, 1.6 M LI2SO4; THEN CRYSTAL WAS SOAKED IN 100 MM HEPES, 500MM FORMATE, PH 7.5, 2.0 M LI2SO4, 1.5 MM NICL2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 27738 / % possible obs: 100 % / Redundancy: 4.1 % / Rsym value: 0.117 / Net I/σ(I): 9.996 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.393 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.117 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.393 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.5→10 Å / σ(F): 0 Details: ALL NON-BONDED INTERACTIONS INVOLVING THE NICKEL IONS OR FORMATE ION WERE REMOVED DURING REFINEMENT THE OCCUPANCIES FOR THE NICKEL IONS WERE REFINED WITH A FIXED B-FACTOR OF 17 (ANGSTROMS)**2.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|