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Yorodumi- PDB-6i9y: The 2.14 A X-ray crystal structure of Sporosarcina pasteurii urea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i9y | ||||||
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Title | The 2.14 A X-ray crystal structure of Sporosarcina pasteurii urease in complex with Au(I) ions | ||||||
Components | (Urease subunit ...) x 3 | ||||||
Keywords | HYDROLASE / urease / nickel / gold compounds / metal-based ndrugs | ||||||
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: 2.14 Å | ||||||
Authors | Mazzei, L. / Cianci, M. / Ciurli, S. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2019 Title: Inhibition Mechanism of Urease by Au(III) Compounds Unveiled by X-ray Diffraction Analysis. Authors: Mazzei, L. / Wenzel, M.N. / Cianci, M. / Palombo, M. / Casini, A. / Ciurli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i9y.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i9y.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 6i9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i9y_validation.pdf.gz | 476.6 KB | Display | wwPDB validaton report |
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Full document | 6i9y_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 6i9y_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 6i9y_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/6i9y ftp://data.pdbj.org/pub/pdb/validation_reports/i9/6i9y | HTTPS FTP |
-Related structure data
Related structure data | 5g4hS S: Starting model for refinement |
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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 ABC
#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: 61575.648 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 , 6 types, 359 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-OH / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 2.81 Å3/Da / Density % sol: 56.24 % / Description: Rice-shaped crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: The protein-ligand complex in 50 mM HEPES buffer, pH 7.50 (also containing 5% (v/v) DMSO), was diluted with an equal volume of 1.5 M ammonium sulfate containing the same concentration of ligand and DMSO. PH range: 6.3-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 21, 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: 2.14→45.8 Å / Num. obs: 54809 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.07 / Rrim(I) all: 0.157 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.509 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4421 / CC1/2: 0.627 / Rpim(I) all: 0.785 / Rrim(I) all: 1.71 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G4H Resolution: 2.14→45.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.715 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.163
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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: 40.28 Å2
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Refinement step | Cycle: 1 / Resolution: 2.14→45.8 Å
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