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Yorodumi- PDB-7d5j: CRYSTAL STRUCTURE OF R220A VARIANT PENA BETA-LACTAMASE FROM BURKH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d5j | ||||||
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Title | CRYSTAL STRUCTURE OF R220A VARIANT PENA BETA-LACTAMASE FROM BURKHOLDERIA MULTIVORANS | ||||||
Components | PenA Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / drug-resistant / antibiotics | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Burkholderia multivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Nukaga, M. / Hoshino, T. / Papp-Wallace, K.M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2021 Title: Assessing the Potency of beta-Lactamase Inhibitors with Diverse Inactivation Mechanisms against the PenA1 Carbapenemase from Burkholderia multivorans . Authors: Nukaga, M. / Yoon, M.J. / Taracilia, M.A. / Hoshino, T. / Becka, S.A. / Zeiser, E.T. / Johnson, J.R. / Papp-Wallace, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d5j.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d5j.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 7d5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d5j_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 7d5j_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 7d5j_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7d5j_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/7d5j ftp://data.pdbj.org/pub/pdb/validation_reports/d5/7d5j | HTTPS FTP |
-Related structure data
Related structure data | 3w4qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31676.922 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: R220A variant Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria) Gene: PenA1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3KN52, beta-lactamase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.95 Å3/Da / Density % sol: 36.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 250microL reservoir (25% polyethylene glycol 8kDa (PEG 8000), 0.1 M MES at pH 6.5)), 4microL hanging drop (7.5 mg/ml protein, 12.5% PEG 8000, 0.05M MES at pH 6.5). Adding Acetone to the drop ...Details: 250microL reservoir (25% polyethylene glycol 8kDa (PEG 8000), 0.1 M MES at pH 6.5)), 4microL hanging drop (7.5 mg/ml protein, 12.5% PEG 8000, 0.05M MES at pH 6.5). Adding Acetone to the drop (final 4%) improved the crystal size and shape. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→42.27 Å / Num. obs: 114986 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.78 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Rrim(I) all: 0.064 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.51→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5243 / Rpim(I) all: 0.218 / Rrim(I) all: 0.427 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W4Q Resolution: 1.51→42.27 Å / SU ML: 0.1358 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 19.7586 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→42.27 Å
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Refine LS restraints |
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LS refinement shell |
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