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Yorodumi- PDB-6afo: Crystal structure of class A b-lactamase, PenL, variant Asn136Asp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6afo | ||||||
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Title | Crystal structure of class A b-lactamase, PenL, variant Asn136Asp, from Burkholderia thailandensis | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / extended-spectrum beta-lactam / Asn136Asp / PenL / Burkhodelria | ||||||
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: 1.399 Å | ||||||
Authors | Cao, T.-P. / Choi, J.M. / Lee, S.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Front Mol Biosci / Year: 2020 Title: Non-catalytic-Region Mutations Conferring Transition of Class A beta-Lactamases Into ESBLs. Authors: Cao, T.-P. / Yi, H. / Dhanasingh, I. / Ghosh, S. / Choi, J.M. / Lee, K.H. / Ryu, S. / Kim, H.S. / Lee, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6afo.cif.gz | 233.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6afo.ent.gz | 185.5 KB | Display | PDB format |
PDBx/mmJSON format | 6afo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6afo_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 6afo_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 6afo_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 6afo_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/6afo ftp://data.pdbj.org/pub/pdb/validation_reports/af/6afo | HTTPS FTP |
-Related structure data
Related structure data | 6afmC 6afnC 6afpC 5gl9S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28678.441 Da / Num. of mol.: 2 / Mutation: N136D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H35_31635 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A2Z4SUB5, UniProt: Q2T5A3*PLUS, beta-lactamase #2: Water | ChemComp-HOH / | Sequence details | N136D is isolated from bacterial colonies that resisted to antibiotic, thus the mutation was not ...N136D is isolated from bacterial colonies that resisted to antibiotic, thus the mutation was not actually engineered using artificial method like site-directed mutagenesis. | |
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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: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium acetate pH 5.0 200 mM sodium chloride 25% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97954 Å |
Detector | Type: ADSC QUANTUM 315r / 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: 0.97954 Å / Relative weight: 1 |
Reflection | Resolution: 1.399→50 Å / Num. obs: 86131 / % possible obs: 99 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.23 |
Reflection shell | Resolution: 1.399→1.42 Å / Rmerge(I) obs: 0.271 / Num. unique obs: 4254 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GL9 Resolution: 1.399→31.772 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 16.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.399→31.772 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.2999 Å / Origin y: 8.0324 Å / Origin z: 17.2013 Å
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Refinement TLS group | Selection details: all |