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Yorodumi- PDB-6zny: 1.50 A resolution 3-methylcatechol (3-methylbenzene-1,2-diol) inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zny | ||||||
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Title | 1.50 A resolution 3-methylcatechol (3-methylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease | ||||||
Components | (Urease subunit ...) x 3 | ||||||
Keywords | METAL BINDING PROTEIN / urease / nickel / enzyme / inhibitor | ||||||
Function / homology | Function and homology information urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sporosarcina pasteurii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mazzei, L. / Cianci, M. / Musiani, F. / Ciurli, S. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zny.cif.gz | 199.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zny.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zny_validation.pdf.gz | 490.5 KB | Display | wwPDB validaton report |
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Full document | 6zny_full_validation.pdf.gz | 494.4 KB | Display | |
Data in XML | 6zny_validation.xml.gz | 38 KB | Display | |
Data in CIF | 6zny_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/6zny ftp://data.pdbj.org/pub/pdb/validation_reports/zn/6zny | HTTPS FTP |
-Related structure data
Related structure data | 6znzC 6zo0C 6zo1C 6zo2C 6zo3C 5g4hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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) Sporosarcina pasteurii (bacteria) / References: UniProt: A0A0H3YGY5, urease |
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#2: Protein | Mass: 13529.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / References: UniProt: P41021, urease |
#3: Protein | Mass: 61697.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) References: UniProt: A0A0H3YL32, UniProt: P41020*PLUS, urease |
-Non-polymers , 5 types, 753 molecules
#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 | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % / 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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2016 |
Radiation | Monochromator: Si(111)Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→113.949 Å / Num. obs: 153039 / % possible obs: 99.7 % / Redundancy: 15.4 % / Biso Wilson estimate: 15.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.042 / Rrim(I) all: 0.121 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 14.9 % / Rmerge(I) obs: 2.359 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7425 / CC1/2: 0.687 / Rpim(I) all: 0.9 / Rrim(I) all: 2.526 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G4H Resolution: 1.5→94.862 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.305 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.052 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: 21.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→94.862 Å
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Refine LS restraints |
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LS refinement shell |
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