+Open data
-Basic information
Entry | Database: PDB / ID: 3v3s | ||||||
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Title | Crystal structure of GES-18 | ||||||
Components | Extended spectrum beta-lactamase GES-18 | ||||||
Keywords | HYDROLASE / Beta lactamase fold / Beta Lactams | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Delbruck, H. / Hoffmann, K.M.V. / Bebrone, C. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2013 Title: GES-18, a new carbapenem-hydrolyzing GES-Type beta-lactamase from pseudomonas aeruginosa that contains Ile80 and Ser170 residues. Authors: Bebrone, C. / Bogaerts, P. / Delbruck, H. / Bennink, S. / Kupper, M.B. / Rezende de Castro, R. / Glupczynski, Y. / Hoffmann, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v3s.cif.gz | 227.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v3s.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 3v3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v3s_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 3v3s_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 3v3s_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 3v3s_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/3v3s ftp://data.pdbj.org/pub/pdb/validation_reports/v3/3v3s | HTTPS FTP |
-Related structure data
Related structure data | 2qpnS 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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Unit cell |
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-Components
#1: Protein | Mass: 31236.492 Da / Num. of mol.: 2 / Fragment: BETA-LACTAMASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: pa41437 / Gene: blaGes / Plasmid: pET28-GES18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: H2ERK4*PLUS, beta-lactamase #2: 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: 2.15 Å3/Da / Density % sol: 42.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 0.02 M citric acid, 0.08 M Bis-Tris propane, 10 % PEG 3350 , pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 21, 2011 / Details: mirror |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→25 Å / Num. all: 43240 / Num. obs: 43240 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.046 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.87→1.97 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 5966 / Rsym value: 0.267 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QPN Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.827 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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