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Yorodumi- PDB-6w2z: Crystal Structure of the Beta Lactamase Class A PenP from Bacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w2z | ||||||
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Title | Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta lactamase class A / Inhibitor / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w2z.cif.gz | 253.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w2z.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 6w2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/6w2z ftp://data.pdbj.org/pub/pdb/validation_reports/w2/6w2z | HTTPS FTP |
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-Related structure data
Related structure data | 6ni1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 30101.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: penP, BSU18800 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P39824, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-FMT / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.96 Å3/Da / Density % sol: 37.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 50 mM Bicine pH 8.8, 2.9 %(v/v), 25.7 %(w/v) PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 71543 / % possible obs: 95.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 3249 / CC1/2: 0.528 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 6NI1 Resolution: 1.5→27.1 Å / SU ML: 0.1782 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.3077
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→27.1 Å
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Refine LS restraints |
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LS refinement shell |
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