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Yorodumi- PDB-3q7v: Beta-Lactam-Sensor Domain of BlaR1 (Apo) from Staphylococcus Aure... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q7v | ||||||
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Title | Beta-Lactam-Sensor Domain of BlaR1 (Apo) from Staphylococcus Aureus with Carboxylated Lys392 | ||||||
Components | (Beta-lactamase regulatory protein BlaR1) x 2 | ||||||
Keywords | HYDROLASE REGULATOR / antibiotic-binding / MRSA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Borbulevych, O.Y. / Mobashery, S. / Baker, B.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Lysine Nzeta-decarboxylation switch and activation of the beta-lactam sensor domain of BlaR1 protein of methicillin-resistant Staphylococcus aureus. Authors: Borbulevych, O. / Kumarasiri, M. / Wilson, B. / Llarrull, L.I. / Lee, M. / Hesek, D. / Shi, Q. / Peng, J. / Baker, B.M. / Mobashery, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q7v.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q7v.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 3q7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/3q7v ftp://data.pdbj.org/pub/pdb/validation_reports/q7/3q7v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29585.252 Da / Num. of mol.: 1 / Fragment: residues 332-583 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1, VRA0048 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WU28 | ||||
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#2: Protein | Mass: 29628.256 Da / Num. of mol.: 1 / Fragment: residues 332-583 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: blaR1, VRA0048 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WU28 | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: 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: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG4000 30%, TRIS 0.1M, NH4SSO4 0.2M, pH 8.5, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 30928 / Num. obs: 30186 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.548 / % possible all: 81.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2312 / WRfactor Rwork: 0.1679 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8444 / SU B: 12.404 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2461 / SU Rfree: 0.2033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.203 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.9 Å2 / Biso mean: 28.6695 Å2 / Biso min: 10.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.099→2.153 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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