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Yorodumi- PDB-5gld: Crystal structure of the class A beta-lactamase PenL-tTR11 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gld | |||||||||
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Title | Crystal structure of the class A beta-lactamase PenL-tTR11 in complex with CBA | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / omega-loop | |||||||||
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: 1.7 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 | 5gld.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gld.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gld_validation.pdf.gz | 758.1 KB | Display | wwPDB validaton report |
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Full document | 5gld_full_validation.pdf.gz | 764.2 KB | Display | |
Data in XML | 5gld_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5gld_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/5gld ftp://data.pdbj.org/pub/pdb/validation_reports/gl/5gld | HTTPS FTP |
-Related structure data
Related structure data | 5gl9SC 5glaC 5glbC 5glcC 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: 30777.803 Da / Num. of mol.: 1 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 | ChemComp-CB4 / |
#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: 1.93 Å3/Da / Density % sol: 36.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEGMME2000, 0.1M K-thiocyanate, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2013 |
Radiation | Monochromator: DCM Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 26638 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.093 / Net I/av σ(I): 27.482 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 9.532 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GL9 Resolution: 1.7→34.222 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→34.222 Å
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Refine LS restraints |
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LS refinement shell |
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