[English] 日本語
![](img/lk-miru.gif)
- PDB-7b59: X-ray crystal structure of Sporosarcina pasteurii urease inhibite... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7b59 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Br determined at 1.63 Angstroms | |||||||||
![]() | (Urease subunit ...) x 3 | |||||||||
![]() | HYDROLASE / urease / enzyme / nickel / silver | |||||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mazzei, L. / Cianci, M. / Ciurli, S. | |||||||||
![]() | ![]() Title: Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. Authors: Mazzei, L. / Cirri, D. / Cianci, M. / Messori, L. / Ciurli, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 198.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 56.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b58C ![]() 7b5aC ![]() 6g48S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
-Urease subunit ... , 3 types, 3 molecules AAABBBCCC
#1: Protein | Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Protein | Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 61575.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 743 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/O.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/O.gif)
![](data/chem/img/AG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-O / | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % / Description: Rice-shaped |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: THE PROTEIN-LIGAND (600 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME ...Details: THE PROTEIN-LIGAND (600 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO. PH range: 6.3-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Monochromator: SI(111) SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→113.8 Å / Num. obs: 119894 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.043 / Rrim(I) all: 0.138 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 18.4 % / Rmerge(I) obs: 4.326 / Mean I/σ(I) obs: 1 / Num. unique obs: 5831 / CC1/2: 0.702 / Rpim(I) all: 1.47 / Rrim(I) all: 4.572 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6G48 Resolution: 1.63→113.8 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.345 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.073 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.432 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→113.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|