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Yorodumi- PDB-8ep6: Crystal Structure of the Beta-lactamase Class D from Chitinophaga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ep6 | ||||||
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Title | Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in complex with Avibactam | ||||||
Components | Beta-lactamase Class D Cpin_0907 | ||||||
Keywords | HYDROLASE/INHIBITOR / beta lactamase class D / avibactam / antibiotic resistance / transpeptidase / Center for Structural Biology of Infectious Diseases / CSBID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ACETIC ACID / Chem-NXL Function and homology information | ||||||
Biological species | Chitinophaga pinensis DSM 2588 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in the complex with Avibactam. Authors: Maltseva, N. / Kim, Y. / Endres, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ep6.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ep6.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ep6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8ep6 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8ep6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29607.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chitinophaga pinensis DSM 2588 (bacteria) Strain: DSM 2588 / Gene: blaOXA, FEF09_01595 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold |
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#2: Chemical | ChemComp-NXL / ( |
#3: Chemical | ChemComp-ACY / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 37.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M imidazole, pH 6.5, 0.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 37009 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.55 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.056 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1838 / CC1/2: 0.769 / Rpim(I) all: 0.375 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→34.35 Å / SU ML: 0.1413 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.9991 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.35 Å
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Refine LS restraints |
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LS refinement shell |
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