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- PDB-6r79: Structure of IMP-13 metallo-beta-lactamase in apo form (loop open) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r79 | ||||||||||||
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Title | Structure of IMP-13 metallo-beta-lactamase in apo form (loop open) | ||||||||||||
![]() | Beta-lactamase | ||||||||||||
![]() | HYDROLASE / metallo-beta-lactamase beta-lactamase | ||||||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Zak, K.M. / Softley, C. / Kolonko, M. / Sattler, M. / Popowicz, G.M. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure and Molecular Recognition Mechanism of IMP-13 Metallo-beta-Lactamase. Authors: Softley, C.A. / Zak, K.M. / Bostock, M.J. / Fino, R. / Zhou, R.X. / Kolonko, M. / Mejdi-Nitiu, R. / Meyer, H. / Sattler, M. / Popowicz, G.M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208 KB | Display | ![]() |
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PDB format | ![]() | 160.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 500.7 KB | Display | ![]() |
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Full document | ![]() | 512.3 KB | Display | |
Data in XML | ![]() | 45.4 KB | Display | |
Data in CIF | ![]() | 65.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r73C ![]() 6r78SC ![]() 6rzrC ![]() 6rzsC ![]() 6s0hC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24567.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 930 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-GLY / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→61.55 Å / Num. obs: 67023 / % possible obs: 94.65 % / Redundancy: 1.7 % / CC1/2: 0.997 / Net I/σ(I): 9.58 |
Reflection shell | Resolution: 1.9→1.968 Å / Num. unique obs: 6850 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6R78 Resolution: 1.9→61.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.608 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1638 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.145
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.68 Å2 / Biso mean: 29.658 Å2 / Biso min: 12.35 Å2
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Refinement step | Cycle: final / Resolution: 1.9→61.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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