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Yorodumi- PDB-4u0x: Structure of ADC-7 beta-lactamase in complex with boronic acid in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u0x | ||||||
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Title | Structure of ADC-7 beta-lactamase in complex with boronic acid inhibitor S02030 | ||||||
Components | ADC-7 beta-lactamase | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / beta-lactamase / boronic acid inhibitor / Hydrolase-Hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Powers, R.A. / Wallar, B.J. / Swanson, H.C. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Biochemical and Structural Analysis of Inhibitors Targeting the ADC-7 Cephalosporinase of Acinetobacter baumannii. Authors: Powers, R.A. / Swanson, H.C. / Taracila, M.A. / Florek, N.W. / Romagnoli, C. / Caselli, E. / Prati, F. / Bonomo, R.A. / Wallar, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u0x.cif.gz | 302.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u0x.ent.gz | 244 KB | Display | PDB format |
PDBx/mmJSON format | 4u0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0x ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0x | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 40677.301 Da / Num. of mol.: 4 / Fragment: UNP residues 24-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DRA1, beta-lactamase #2: Chemical | ChemComp-ZXM / #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 1500, succinate, phosphate, glycine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→81.198 Å / Num. obs: 91079 / % possible obs: 100 % / Redundancy: 3.9 % / Net I/σ(I): 3.29 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.998 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.19 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.323 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→50 Å
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