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Yorodumi- PDB-3ly3: Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ly3 | ||||||
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Title | Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / fluorophore / biosensor / Antibiotic resistance / Cell membrane / Lipoprotein / Membrane / Palmitate | ||||||
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: 1.8 Å | ||||||
Authors | Zhao, Y.X. / Leung, Y.C. / Wong, W.T. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of fluorophore-labeled Class A Beta-lactamase PenP Authors: Zhao, Y.X. / Leung, Y.C. / Wong, W.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ly3.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ly3.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ly3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/3ly3 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/3ly3 | HTTPS FTP |
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-Related structure data
Related structure data | 4blmS 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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Unit cell |
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-Components
#1: Protein | Mass: 28839.645 Da / Num. of mol.: 1 / Fragment: residues 47-303 / Mutation: E166C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: 749/C / Gene: penP / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00808, beta-lactamase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF |
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Detector | Date: Jul 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.5→54.4 Å / Num. obs: 33021 / Rmerge(I) obs: 0.059 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BLM Resolution: 1.8→39.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.479 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.15 / 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: 25.052 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→39.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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