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Yorodumi- PDB-5zyb: Crystal structure of MOX-1 complexed with a boronic acid transiti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zyb | ||||||
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Title | Crystal structure of MOX-1 complexed with a boronic acid transition state inhibitor S02030 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / serine beta-lactamase / inhibitor | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Shimizu-Ibuka, A. / Furukawa, N. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of MOX-1 complexed with a boronic acid transition state inhibitor S02030 Authors: Ishikawa, T. / Furukawa, N. / Caselli, E. / Prati, F. / Taracila, M.A. / Bonomo, R.A. / Ishii, Y. / Shimizu-Ibuka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zyb.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zyb.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/5zyb ftp://data.pdbj.org/pub/pdb/validation_reports/zy/5zyb | HTTPS FTP |
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-Related structure data
Related structure data | 3w8kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40589.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaMOX-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51578, beta-lactamase | ||||
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#2: Chemical | ChemComp-ZXM / | ||||
#3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, 100 mM sodium cacodylate buffer (pH 6.5), 0.2 M zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→61.51 Å / Num. obs: 20024 / % possible obs: 99.9 % / Redundancy: 3.2 % / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.13→2.18 Å / Num. unique obs: 1397 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W8K Resolution: 2.13→42.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.046 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.173 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.931 Å2
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Refinement step | Cycle: 1 / Resolution: 2.13→42.69 Å
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Refine LS restraints |
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