+Open data
-Basic information
Entry | Database: PDB / ID: 1s3t | ||||||
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Title | BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE | ||||||
Components |
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Keywords | HYDROLASE / UREASE / BACILLUS PASTEURII / NICKEL / METALLOENZYME / borate | ||||||
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: 2.1 Å | ||||||
Authors | Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2004 Title: Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism. Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S. / Ciurli, S. #1: Journal: J.Biol.Inorg.Chem. / Year: 2001 Title: Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights Into the Enzyme Mechanism Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Ciurli, S. / Mangani, S. #2: Journal: J.Biol.Inorg.Chem. / Year: 2000 Title: The Complex of Bacillus Pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 A Resolution Authors: Benini, S. / Rypniewski, W.R. / Wilson, K.S. / Miletti, S. / Ciurli, S. / Mangani, S. #3: 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. #4: 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. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. / Mangani, S. #5: 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. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICALLY FUNCTIONAL MOLECULE IS A TRIMER. | ||||||
Remark 999 | SEQUENCE THE AUTHOR STATES THAT THE RESIDUES LISTED IN SEQADV ARE WHAT IS SEEN IN THE DENSITY, AND ...SEQUENCE THE AUTHOR STATES THAT THE RESIDUES LISTED IN SEQADV ARE WHAT IS SEEN IN THE DENSITY, AND IT IS NOT CLEAR WHERE THE DISCREPANCIES ARISE FROM. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s3t.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s3t.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/1s3t ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s3t | HTTPS FTP |
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-Related structure data
Related structure data | 2ubpS 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
-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) / Strain: dsm33 / References: UniProt: P41022, urease |
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#2: Protein | Mass: 13975.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sporosarcina pasteurii (bacteria) / Strain: dsm33 / 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) / Strain: dsm33 / References: UniProt: P41020, urease |
-Non-polymers , 4 types, 410 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-BO3 / | #7: 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: 54.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 1.8 M AMS, 100 mM citric acid, 100 mM boric acid , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 21, 2002 / Details: Bent mirror |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.8 Å / Num. all: 56339 / Num. obs: 56215 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.16 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.56 / Num. unique all: 2104 / Rsym value: 0.547 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ubp Resolution: 2.1→24.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.449 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.175 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.624 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→24.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.156 Å / Total num. of bins used: 20 /
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