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Yorodumi- PDB-5zft: Crystal structure of beta-lactamase PenP mutant-E166Y in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zft | ||||||
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Title | Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "pre-deacylation" intermediate | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / class A beta-lactamase / antibiotic resistance | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Pan, X. / Zhao, Y. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: The hydrolytic water molecule of Class A beta-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis. Authors: He, Y. / Lei, J. / Pan, X. / Huang, X. / Zhao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zft.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zft.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zft ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zft | HTTPS FTP |
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-Related structure data
Related structure data | 5zflC 5zg6C 4blmS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29861.859 Da / Num. of mol.: 2 / Mutation: E166Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P00808, beta-lactamase #2: Chemical | #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: 1.97 Å3/Da / Density % sol: 37.52 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris pH8.0, 25% PEG 33500, 4M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→42.49 Å / Num. obs: 32004 / % possible obs: 92.8 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.03 / Rrim(I) all: 0.059 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 8.4 / CC1/2: 0.981 / Rpim(I) all: 0.079 / Rrim(I) all: 0.156 / % possible all: 87.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BLM Resolution: 1.93→35.1 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.166 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.767 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→35.1 Å
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