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- PDB-3pae: Crystal structure of the K84D mutant of OXA-24/40 in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pae | ||||||
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Title | Crystal structure of the K84D mutant of OXA-24/40 in complex with doripenem | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE/ANTIBIOTIC / hydrolase / carbapenemase / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Powers, R.A. / Leonard, D.A. / Schneider, K.D. | ||||||
![]() | ![]() Title: Structures of the Class D Carbapenemase OXA-24 from Acinetobacter baumannii in Complex with Doripenem. Authors: Schneider, K.D. / Ortega, C.J. / Renck, N.A. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A. #1: ![]() Title: The 1.4 A crystal structure of the class D beta-lactamase OXA-1 complexed with doripenem Authors: Schneider, K.D. / Karpen, M.E. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.9 KB | Display | ![]() |
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PDB format | ![]() | 90.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pagC ![]() 2jc7S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27660.760 Da / Num. of mol.: 2 / Fragment: UNP residues 32-275 / Mutation: K84D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40 Plasmid: pET24a / Production host: ![]() ![]() |
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#2: Chemical | |
#3: Chemical | |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
Nonpolymer details | 4J6 IN THE STRUCTURE REPRESENTS THE DELTA 2 TAUTOMER, IN WHICH A DOUBLE BOND IS PRESENT BETWEEN ...4J6 IN THE STRUCTURE REPRESENTS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.58 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 100 mM TRIS-HCl, 2.0 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 50780 / % possible obs: 98.8 % |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2JC7 Resolution: 2.1→31.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.899 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.147 / 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: 37.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→31.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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