+Open data
-Basic information
Entry | Database: PDB / ID: 1bqb | ||||||
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Title | AUREOLYSIN, STAPHYLOCOCCUS AUREUS METALLOPROTEINASE | ||||||
Components | PROTEIN (AUREOLYSIN) | ||||||
Keywords | HYDROLASE / METALLOPROTEINASE | ||||||
Function / homology | Function and homology information aureolysin / metalloendopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Medrano, F.J. / Banbula, A. / Potempa, J. / Travis, J. / Bode, W. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Amino-acid sequence and three-dimensional structure of the Staphylococcus aureus metalloproteinase at 1.72 A resolution. Authors: Banbula, A. / Potempa, J. / Travis, J. / Fernandez-Catalan, C. / Mann, K. / Huber, R. / Bode, W. / Medrano, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bqb.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bqb.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bqb ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bqb | HTTPS FTP |
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-Related structure data
Related structure data | 1lnfS 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
#1: Protein | Mass: 33358.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: V8-BC10 / References: UniProt: P81177, thermolysin | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.79 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.2 / Details: 0.1 M SODIUM ACETATE PH 5.2 AND 40% PEG 4000 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 284 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→15 Å / Num. obs: 27738 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.72→1.78 Å / % possible all: 86.4 |
Reflection | *PLUS Num. measured all: 120813 |
Reflection shell | *PLUS % possible obs: 86.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LNF Resolution: 1.72→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.72→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.38 |