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Yorodumi- PDB-1xa1: Crystal structure of the sensor domain of BlaR1 from Staphylococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xa1 | ||||||
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Title | Crystal structure of the sensor domain of BlaR1 from Staphylococcus aureus in its apo form | ||||||
Components | Regulatory protein blaR1 | ||||||
Keywords | SIGNALING PROTEIN / beta-lactamase / BlaR1 / sensor domain / staphylococcus aureus / antibiotic resistance | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wilke, M.S. / Hills, T.L. / Zhang, H.Z. / Chambers, H.F. / Strynadka, N.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structures of the Apo and penicillin-acylated forms of the BlaR1 beta-lactam sensor of Staphylococcus aureus. Authors: Wilke, M.S. / Hills, T.L. / Zhang, H.Z. / Chambers, H.F. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xa1.cif.gz | 232.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xa1.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xa1 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xa1 | HTTPS FTP |
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-Related structure data
Related structure data | 1xa7SC 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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Unit cell |
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-Components
#1: Protein | Mass: 30001.791 Da / Num. of mol.: 4 / Fragment: C-terminal Domain (residues 331-585) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1 / Plasmid: pET41b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P18357 #2: Chemical | #3: Chemical | ChemComp-POP / #4: 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: 2.2 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 18-23% PEG 3350, 0.2M NaH2PO4, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 95274 / Num. obs: 95274 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: benzylpenicillin-acylated BlaR1 C-terminal domain, PDB entry 1XA7 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.958 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.134 / 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: 18.616 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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