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Yorodumi- PDB-7b5a: X-ray crystal structure of Sporosarcina pasteurii urease inhibite... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b5a | ||||||
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Title | X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)2NO3 determined at 1.97 Angstroms | ||||||
Components | (Urease subunit ...) x 3 | ||||||
Keywords | HYDROLASE / urease / enzyme / nickel / silver | ||||||
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: 1.97 Å | ||||||
Authors | Mazzei, L. / Cianci, M. / Ciurli, S. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2021 Title: Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. Authors: Mazzei, L. / Cirri, D. / Cianci, M. / Messori, L. / Ciurli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b5a.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b5a.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b5a_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7b5a_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7b5a_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 7b5a_validation.cif.gz | 51.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5a ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5a | HTTPS FTP |
-Related structure data
Related structure data | 7b58C 7b59C 6g48S 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: P41022, 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: P41020, urease |
-Non-polymers , 6 types, 501 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-O / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.74 Å3/Da / Density % sol: 55.14 % / Description: Rice-shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: THE PROTEIN-LIGAND (300 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME ...Details: THE PROTEIN-LIGAND (300 microM) COMPLEX IN 50 mM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 1% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.4 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO. PH range: 6.3-6.8 |
-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: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→113.87 Å / Num. obs: 68762 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.064 / Rrim(I) all: 0.234 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 12.4 % / Rmerge(I) obs: 3.191 / Mean I/σ(I) obs: 1 / Num. unique obs: 4556 / CC1/2: 0.593 / Rpim(I) all: 0.982 / Rrim(I) all: 3.473 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6G48 Resolution: 1.97→97.798 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.99 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.135 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: 37.581 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→97.798 Å
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Refine LS restraints |
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LS refinement shell |
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