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- PDB-6zo0: 2.23 A resolution 3,4-dimethylcatechol (3,4-dimethylbenzene-1,2-d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zo0 | ||||||
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Title | 2.23 A resolution 3,4-dimethylcatechol (3,4-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease | ||||||
![]() | (Urease subunit ...) x 3 | ||||||
![]() | METAL BINDING PROTEIN / urease / nickel / enzyme / inhibitor | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S. | ||||||
![]() | ![]() Title: Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Authors: Mazzei, L. / Contaldo, U. / Musiani, F. / Cianci, M. / Bagnolini, G. / Roberti, M. / 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 | ![]() | 190.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.2 KB | Display | ![]() |
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Full document | ![]() | 494.4 KB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6znyC ![]() 6znzC ![]() 6zo1C ![]() 6zo2C ![]() 6zo3C ![]() 5g4hS 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 AAABBBCCC
#1: Protein | Mass: 11134.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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: 61713.812 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, 426 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-OH / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.36 % / 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 |
-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: Feb 21, 2020 |
Radiation | Monochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→188.71 Å / Num. obs: 47585 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.125 / Rrim(I) all: 0.299 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.23→2.3 Å / Redundancy: 11 % / Rmerge(I) obs: 1.751 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4300 / CC1/2: 0.657 / Rpim(I) all: 0.804 / Rrim(I) all: 1.929 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G4H Resolution: 2.23→113.883 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.124 / SU B: 7.2 / SU ML: 0.163 / Average fsc free: 0.8889 / Average fsc work: 0.9054 / Cross valid method: FREE R-VALUE / ESU R: 0.223 / ESU R Free: 0.19 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.357 Å2
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Refinement step | Cycle: LAST / Resolution: 2.23→113.883 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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