+Open data
-Basic information
Entry | Database: PDB / ID: 6v1p | ||||||
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Title | Structure of VIM-2 bound to QPX7728 at 1.20 A | ||||||
Components | Beta-lactamase class B VIM-2 | ||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / carbapenemase / boronate / inhibitor / beta-lactamase / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Pemberton, O.A. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases. Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. ...Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. / Glinka, T.W. / Pemberton, O.A. / Chen, Y. / Dudley, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v1p.cif.gz | 222.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v1p.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 6v1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v1p_validation.pdf.gz | 410.3 KB | Display | wwPDB validaton report |
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Full document | 6v1p_full_validation.pdf.gz | 411.1 KB | Display | |
Data in XML | 6v1p_validation.xml.gz | 2 KB | Display | |
Data in CIF | 6v1p_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/6v1p ftp://data.pdbj.org/pub/pdb/validation_reports/v1/6v1p | HTTPS FTP |
-Related structure data
Related structure data | 6v1jC 6v1mC 6v1oC 1ko3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0 |
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-Non-polymers , 5 types, 604 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.84 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.17 M Ammonium acetate, 0.085 M Sodium acetate pH 4.6, 25.5% (w/v) PEG4000, 15% (v/v) Glycerol, 1 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→42.54 Å / Num. obs: 122856 / % possible obs: 96.5 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 5.3 % / Rmerge(I) obs: 2.019 / Num. measured all: 24912 / Num. unique obs: 4666 / CC1/2: 0.457 / Net I/σ(I) obs: 1.7 / % possible all: 75.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KO3 Resolution: 1.2→35.2 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.44 Å2 / Biso mean: 17.7143 Å2 / Biso min: 5.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→35.2 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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