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- PDB-6h8j: 1.45 A resolution of Sporosarcina pasteurii urease inhibited in t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h8j | ||||||
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Title | 1.45 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPTO | ||||||
![]() | (Urease subunit ...) x 3 | ||||||
![]() | HYDROLASE | ||||||
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: Insights into Urease Inhibition by N-( n-Butyl) Phosphoric Triamide through an Integrated Structural and Kinetic Approach. Authors: Mazzei, L. / Cianci, M. / Contaldo, U. / Ciurli, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357.7 KB | Display | ![]() |
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PDB format | ![]() | 288.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.1 KB | Display | ![]() |
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Full document | ![]() | 495.8 KB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ol4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Urease subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0A0H3YGY5, UniProt: P41022*PLUS, urease |
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#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) ![]() References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease |
-Non-polymers , 5 types, 647 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/2PA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/2PA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-2PA / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % / Description: Rice shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 50 mM citrate buffer at pH 6.3, containing 1.6 - 2.0 M ammonium sulfate as a precipitant PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 13, 2018 |
Radiation | Monochromator: Si(111) silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→48.74 Å / Num. obs: 168094 / % possible obs: 99.1 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8062 / CC1/2: 0.655 / Rpim(I) all: 0.578 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OL4 Resolution: 1.45→48.74 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 2.195 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.045 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.867 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→48.74 Å
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Refine LS restraints |
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