+Open data
-Basic information
Entry | Database: PDB / ID: 5f82 | ||||||
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Title | Apo GES-5 C69G mutant | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / carbapenemase / antibiotic resistance | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.96 Å | ||||||
Authors | Smith, C.A. / Vakulenko, S.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Role of the Conserved Disulfide Bridge in Class A Carbapenemases. Authors: Smith, C.A. / Nossoni, Z. / Toth, M. / Stewart, N.K. / Frase, H. / 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 | 5f82.cif.gz | 353.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f82.ent.gz | 293.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f82_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 5f82_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 5f82_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 5f82_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/5f82 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/5f82 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31176.375 Da / Num. of mol.: 2 / Mutation: C69G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaGES-5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0EL75, beta-lactamase #2: Chemical | #3: 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: 1.93 Å3/Da / Density % sol: 36.3 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M D,L-malic acid, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9495 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 27, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9495 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→37.2 Å / Num. obs: 280826 / % possible obs: 97.6 % / Redundancy: 3.5 % / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 0.96→0.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.2 / % possible all: 73.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→37.192 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 10.91 / 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: 0.96→37.192 Å
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Refine LS restraints |
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LS refinement shell |
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