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- PDB-6rkg: 1.32 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: 6rkg | ||||||
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Title | 1.32 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 7.5 | ||||||
![]() | (Urease subunit ...) x 3 | ||||||
![]() | HYDROLASE / UREA / NICKEL / NBPTO | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mazzei, L. / Cianci, M. / Benini, S. / Ciurli, S. | ||||||
![]() | ![]() Title: The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme. Authors: Mazzei, L. / Cianci, M. / Benini, S. / 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 | ![]() | 357.5 KB | Display | ![]() |
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PDB format | ![]() | 287.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 352.7 KB | Display | ![]() |
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Full document | ![]() | 354.7 KB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rp1C ![]() 5ol4S S: Starting model for refinement C: citing same article ( |
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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, 766 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: 2.76 Å3/Da / Density % sol: 55.51 % / Description: Rice-shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein dissolved in 50 mM HEPES, pH 7.5, 2 mM EDTA, 4 mM NBPTO. Precipitant solution consisting of 100 mM citrate buffer, 1.7-1.9 M ammonium sulfate, 4 mM NBPTO, at pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018 |
Radiation | Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→97.67 Å / Num. obs: 221217 / % possible obs: 98.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.035 / Rrim(I) all: 0.128 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.23 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10653 / CC1/2: 0.653 / Rpim(I) all: 0.633 / Rrim(I) all: 2.392 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OL4 Resolution: 1.32→97.67 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.587 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / 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: 16.396 Å2
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Refinement step | Cycle: 1 / Resolution: 1.32→97.67 Å
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Refine LS restraints |
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