+Open data
-Basic information
Entry | Database: PDB / ID: 6m5h | ||||||
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Title | A class C beta-lactamase mutant - Y150F | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase | ||||||
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 | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Bae, D.W. / Jung, Y.E. / Cha, S.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2020 Title: Novel inhibition mechanism of carbapenems on the ACC-1 class C beta-lactamase. Authors: Bae, D.W. / Jung, Y.E. / Jeong, B.G. / 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 | 6m5h.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m5h.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 6m5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/6m5h ftp://data.pdbj.org/pub/pdb/validation_reports/m5/6m5h | HTTPS FTP |
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-Related structure data
Related structure data | 6m5pC 6m5qC 6k8xS 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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Unit cell |
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-Components
#1: Protein | Mass: 40697.316 Da / Num. of mol.: 1 / Mutation: Y150F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla-ACC-1, acc-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XB24, beta-lactamase |
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#2: 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: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 30% polyethylene glycol 1500, 0.1M sodium cacodylate (pH 5.5), 0.2M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→50 Å / Num. obs: 430004 / % possible obs: 96.7 % / Redundancy: 3.35 % / Rsym value: 0.01 / Net I/σ(I): 6.54 |
Reflection shell | Resolution: 0.98→4.39 Å / Num. unique obs: 30255 / CC1/2: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6K8X Resolution: 1.2→32.99 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Displacement parameters | Biso mean: 14.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→32.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.255 Å
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