+Open data
-Basic information
Entry | Database: PDB / ID: 5gl9 | |||||||||
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Title | Crystal structure of the class A beta-lactamase PenL | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / PenL / omega loop / Burkholderia | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Burkholderia thailandensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Choi, J.M. / Yi, H. / Kim, H.S. / Lee, S.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A beta-lactamase, PenL Authors: Yi, H. / Choi, J.M. / Hwang, J. / Prati, F. / Cao, T.P. / Lee, S.H. / Kim, H.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gl9.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gl9.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gl9_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 5gl9_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 5gl9_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5gl9_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/5gl9 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/5gl9 | HTTPS FTP |
-Related structure data
Related structure data | 5glaC 5glbC 5glcC 5gldC 1yljS C: citing same article (ref.) 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: 28677.457 Da / Num. of mol.: 1 / Fragment: UNP residues 31-294 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H35_31635 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A2Z4SUB5, UniProt: Q2T5A3*PLUS, beta-lactamase | ||
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#2: Chemical | #3: 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: 2.02 Å3/Da / Density % sol: 39.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 0.1M Li-sulfate, 30%(w/v) PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2012 |
Radiation | Monochromator: DCM Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 37054 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/av σ(I): 73.911 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 35.682 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLJ Resolution: 1.5→27.8 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→27.8 Å
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Refine LS restraints |
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LS refinement shell |
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