+Open data
-Basic information
Entry | Database: PDB / ID: 5joc | ||||||
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Title | Crystal structure of the S61A mutant of AmpC BER | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC Ber / class C beta-lactamase / S61A mutation | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / nucleotide binding / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Na, J.H. / An, Y.J. / Cha, S.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Structural basis for the extended substrate spectrum of AmpC BER and structure-guided discovery of the inhibition activity of citrate against the class C beta-lactamases AmpC BER and CMY-10. Authors: Na, J.H. / Cha, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5joc.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5joc.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 5joc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/5joc ftp://data.pdbj.org/pub/pdb/validation_reports/jo/5joc | HTTPS FTP |
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-Related structure data
Related structure data | 5ggwC 1f1gS 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
#1: Protein | Mass: 40540.031 Da / Num. of mol.: 2 / Mutation: S61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampC / Production host: Escherichia coli (E. coli) References: UniProt: A7TUE6, UniProt: P00811*PLUS, beta-lactamase #2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | |
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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: 3.49 Å3/Da / Density % sol: 64.74 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 25% PEG 3350, 0.1 M Citric Acid, NaOH pH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 109761 / % possible obs: 96.5 % / Redundancy: 5.3 % / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.75→1.78 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F1G Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.156 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / 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: 27.604 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
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Refine LS restraints |
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