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- PDB-3ixb: X-ray crystal structure of the extended-spectrum AmpC E219K mutan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ixb | ||||||
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Title | X-ray crystal structure of the extended-spectrum AmpC E219K mutant beta-lactamase complexed with benzo(b)thiophene-2-boronic acid (BZB) at 1.63 Angstrom resolution | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / serine hydrolase / beta-lactamase / cephalosporinase / extended-spectrum antibiotic resistance / Antibiotic resistance / Periplasm | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Shoichet, B.K. / Thomas, V.L. | ||||||
![]() | ![]() Title: Structural bases for stability-function tradeoffs in antibiotic resistance. Authors: Thomas, V.L. / McReynolds, A.C. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.3 KB | Display | ![]() |
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PDB format | ![]() | 132.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 461.3 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 55 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iwiC ![]() 3iwoC ![]() 3iwqC ![]() 3ixdC ![]() 3ixgC ![]() 3ixhC ![]() 1ke4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39587.988 Da / Num. of mol.: 2 / Mutation: E219K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M KPi, pH 8.7, 360 uM benzo(b)thiophene-2-boronic acid, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2009 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→87.702 Å / Num. all: 97618 / Num. obs: 97467 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rsym value: 0.061 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1KE4 Resolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 1.522 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.538 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 Å / Total num. of bins used: 20
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