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Open data
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Basic information
Entry | Database: PDB / ID: 5fqc | |||||||||
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Title | Crystal structure of the metallo-beta-lactamase VIM-2 with 2C | |||||||||
![]() | BETA-LACTAMASE | |||||||||
![]() | HYDROLASE / ANTIBIOTIC RESISTANCE | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Brem, J. / Cain, R. / McDonough, M.A. / Clifton, I.J. / Fishwick, C.W.G. / Schofield, C.J. | |||||||||
![]() | ![]() Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates. Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.9 KB | Display | ![]() |
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PDB format | ![]() | 163.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fq9C ![]() 5fqbC ![]() 5j8xC ![]() 4bz3S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.0989, -0.0067, 0.9951), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-266 Source method: isolated from a genetically manipulated source Details: 2C BOUND TO THE ACTIVE SITE / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 460 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/OK3.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/OK3.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | CLEAVED N-TERMINAL HISTAG |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.9 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2015 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→28.89 Å / Num. obs: 71728 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 14.52 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BZ3 Resolution: 1.449→28.886 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.449→28.886 Å
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Refine LS restraints |
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LS refinement shell |
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