+Open data
-Basic information
Entry | Database: PDB / ID: 4net | ||||||
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Title | Crystal structure of ADC-1 beta-lactamase | ||||||
Components | AmpC | ||||||
Keywords | HYDROLASE / beta-lactamase / antibiotic resistance / apo enzyme | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Bhattacharya, M. / Toth, M. / Antunes, N.T. / Smith, C.A. / Vakulenko, S.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the extended-spectrum class C beta-lactamase ADC-1 from Acinetobacter baumannii. Authors: Bhattacharya, M. / Toth, M. / Antunes, N.T. / Smith, C.A. / Vakulenko, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4net.cif.gz | 328.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4net.ent.gz | 268.2 KB | Display | PDB format |
PDBx/mmJSON format | 4net.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/4net ftp://data.pdbj.org/pub/pdb/validation_reports/ne/4net | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4R5, beta-lactamase #2: Chemical | ChemComp-NO3 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: unbuffered 0.2 M lithium nitrate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.98093 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Jul 16, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98093 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→38.5 Å / Num. all: 227477 / Num. obs: 227477 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.2→1.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→38.5 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 18.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→38.5 Å
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Refine LS restraints |
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LS refinement shell |
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