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- PDB-7rpa: X-ray crystal structure of OXA-24/40 K84D in complex with meropenem -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rpa | |||||||||
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Title | X-ray crystal structure of OXA-24/40 K84D in complex with meropenem | |||||||||
![]() | Beta-lactamase | |||||||||
![]() | Hydrolase/Inhibitor / acyl-enzyme complex / carbapenemase / HYDROLASE / Hydrolase-Inhibitor complex | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Powers, R.A. / Mitchell, J.M. / June, C.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. Authors: Mitchell, J.M. / June, C.M. / Baggett, V.L. / Lowe, B.C. / Ruble, J.F. / 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 | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 46.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 733.3 KB | Display | ![]() |
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Full document | ![]() | 736 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rp8C ![]() 7rp9C ![]() 7rpbC ![]() 7rpcC ![]() 7rpdC ![]() 7rpeC ![]() 7rpfC ![]() 7rpgC ![]() 3paeS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27660.760 Da / Num. of mol.: 1 / 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, SI89_16690 Plasmid: pET24a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 57 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/MER.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MER.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / |
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#3: Chemical | ChemComp-MER / ( |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-BCT / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 2% v/v PEG 4000, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→86.02 Å / Num. obs: 21722 / % possible obs: 99.8 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.039 / Rrim(I) all: 0.111 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.27→2.282 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.109 / Num. unique obs: 201 / CC1/2: 0.896 / Rpim(I) all: 0.412 / Rrim(I) all: 1.187 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PAE Resolution: 2.27→86.02 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.725 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 129.19 Å2 / Biso mean: 62.96 Å2 / Biso min: 39.83 Å2
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Refinement step | Cycle: final / Resolution: 2.27→86.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.333 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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