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Yorodumi- PDB-3mbz: OXA-24 beta-lactamase complex soaked with 10mM SA4-17 inhibitor f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mbz | ||||||
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Title | OXA-24 beta-lactamase complex soaked with 10mM SA4-17 inhibitor for 15min | ||||||
Components | Betalactamase OXA24 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / beta-lactamase / beta-lactamase inhibitor / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Sampson, J. / van den Akker, F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase Authors: Bou, G. / Santillana, E. / Sheri, A. / Beceiro, A. / Sampson, J.M. / Kalp, M. / Bethel, C.R. / Distler, A.M. / Drawz, S.M. / Pagadala, S.R. / van den Akker, F. / Bonomo, R.A. / Romero, A. / Buynak, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mbz.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mbz.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/3mbz ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mbz | HTTPS FTP |
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-Related 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: 27586.660 Da / Num. of mol.: 1 / Fragment: UNP residues 32-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: bla-OXA-40, blaOXA-24, blaOXA-33, blaOXA-40, oxa-24, oxa40 Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8RLA6, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MXC / ( |
#4: 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: 4.13 Å3/Da / Density % sol: 70.23 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2M (NH3)2SO4, 0.1M Tris pH 8.5, room temperature, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2008 Details: vertically focusing mirror and a horizontally focusing monochromator |
Radiation | Monochromator: vertically focusing mirror and a horizontally focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.29 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 14760 / Num. obs: 13786 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1434 / % possible all: 59.2 |
-Processing
Software | Name: REFMAC / Version: 5.5.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→32.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.906 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.762 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→32.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.67 Å / Total num. of bins used: 20
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