+Open data
-Basic information
Entry | Database: PDB / ID: 7ddm | ||||||||||||
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Title | Crystal Structure of PenA39 beta-Lactamase | ||||||||||||
Components |
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Keywords | HYDROLASE / beta-lactamase | ||||||||||||
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 CGD2 (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||||||||
Authors | Nukaga, M. / Hoshino, T. / Papp-Wallace, K.M. | ||||||||||||
Funding support | Japan, United States, 3items
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Citation | Journal: To Be Published Title: Frameshift mutations in genes encoding PBP3 and PBP4 trigger an unusual, extreme beta-lactam resistance phenotype in Burkholderia multivorans Authors: Nukaga, M. / Becka, S.A. / Zeiser, E.T. / Hoshino, Y. / LiPuma, J.J. / 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 | 7ddm.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ddm.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ddm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ddm_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 7ddm_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 7ddm_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7ddm_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/7ddm ftp://data.pdbj.org/pub/pdb/validation_reports/dd/7ddm | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31581.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia multivorans CGD2 (bacteria) Gene: BURMUCGD2_4198 / Plasmid: pGEX-6p-2 / Details (production host): N-terminal GST tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9BS30, beta-lactamase | ||||||
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#2: Protein/peptide | Mass: 1089.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
#3: Chemical | ChemComp-MPD / ( #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 36.94 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 250 microL reservoir (30% MPD, 12.5% polyethylene glycol 1500, 0.1 M Sodium Acetate buffer pH 4.5) with a 4 microL hanging drop (7.5 mg/ml protein, 15% MPD, 6.3% PEG 1500, 0.05 M sodium ...Details: 250 microL reservoir (30% MPD, 12.5% polyethylene glycol 1500, 0.1 M Sodium Acetate buffer pH 4.5) with a 4 microL hanging drop (7.5 mg/ml protein, 15% MPD, 6.3% PEG 1500, 0.05 M sodium acetate buffer pH 4.5), Loop-mounted crystals were flash-cooled without additional cryoprotectant and kept at 100 K with a nitrogen gas stream. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→38.1 Å / Num. obs: 76919 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 10.36 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 3884 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W4Q Resolution: 1.2→38.1 Å / SU ML: 0.0855 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 12.3556 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: 14.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→38.1 Å
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Refine LS restraints |
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LS refinement shell |
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