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Yorodumi- PDB-1ubp: CRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ubp | ||||||
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Title | CRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WITH BETA-MERCAPTOETHANOL AT 1.65 ANGSTROMS RESOLUTION | ||||||
Components | (UREASE) x 3 | ||||||
Keywords | HYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / BETA-MERCAPTOETHANOL | ||||||
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: 1.65 Å | ||||||
Authors | Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1998 Title: The complex of Bacillus pasteurii urease with beta-mercaptoethanol from X-ray data at 1.65-A resolution Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S. #1: Journal: Structure / Year: 1999 Title: A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels. Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Miletti, S. / Ciurli, S. / Mangani, S. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary high-resolution X-ray diffraction analysis of native and beta-mercaptoethanol-inhibited urease from Bacillus pasteurii. Authors: Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S. #3: Journal: Soil Biol.Biochem. / Year: 1996 Title: Bacillus Pasteurii Urease: A Heteropolymeric Enzyme with a Binuclear Nickel Active Site Authors: Benini, S. / Gessa, C. / Ciurli, S. #4: Journal: Eur.J.Biochem. / Year: 1996 Title: X-ray absorption spectroscopy study of native and phenylphosphorodiamidate-inhibited Bacillus pasteurii urease. Authors: Benini, S. / Ciurli, S. / Nolting, H.F. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ubp.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ubp.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 1ubp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/1ubp ftp://data.pdbj.org/pub/pdb/validation_reports/ub/1ubp | HTTPS FTP |
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-Related structure data
Related structure data | 1kau 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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 11204.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / 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) / Cellular location: CYTOPLASM / References: UniProt: P41021, urease |
#3: Protein | Mass: 61646.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / References: UniProt: P41020, urease |
-Non-polymers , 3 types, 1015 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.3 / Details: pH 6.30 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8855 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 1996 / Details: SEGMENTED MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8855 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→14 Å / Num. obs: 114679 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 10.22 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59 / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 14 Å / Observed criterion σ(I): -3 / Num. measured all: 1172081 |
Reflection shell | *PLUS % possible obs: 97.8 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KAU 1kau Resolution: 1.65→14 Å / σ(F): 0 Details: ALL THE ATOMS WITH OCCUPANCY 0 ARE IN DISORDERED REGIONS OR WITHOUT DENSITY.
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Displacement parameters | Biso mean: 17.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→14 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |