+Open data
-Basic information
Entry | Database: PDB / ID: 6g9t | ||||||
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Title | CRYSTAL STRUCTURE OF CMY-136 class C BETA-LACTAMASE | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / CLASS C BETA-LACTAMASE CMY-136-HisTag / ANTIBIOTIC / DIMER | ||||||
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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Zavala, A. / Retailleau, P. / Naas, T. / Iorga, B. | ||||||
Funding support | France, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2019 Title: Genetic, Biochemical, and Structural Characterization of CMY-136 beta-Lactamase, a Peculiar CMY-2 Variant. Authors: Zavala, A. / Retailleau, P. / Elisee, E. / Iorga, B.I. / Naas, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g9t.cif.gz | 292.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g9t.ent.gz | 236.6 KB | Display | PDB format |
PDBx/mmJSON format | 6g9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/6g9t ftp://data.pdbj.org/pub/pdb/validation_reports/g9/6g9t | HTTPS FTP |
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-Related structure data
Related structure data | 1zc2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41252.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCMY-61 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3F7G9, beta-lactamase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | ChemComp-IPA / #5: 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: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 20 % PEG 4000, 10 % Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.597→50.208 Å / Num. obs: 87503 / % possible obs: 95 % / Redundancy: 4.2 % / Biso Wilson estimate: 17.78 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.049 / Rrim(I) all: 0.105 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.597→1.625 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4345 / CC1/2: 0.749 / Rpim(I) all: 0.348 / Rrim(I) all: 0.76 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZC2 Resolution: 1.6→16.1 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.886 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.114
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Displacement parameters | Biso mean: 19.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→16.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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Refinement TLS params. | S33: -0.0183 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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