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Yorodumi- PDB-5i63: Crystal structure of TEM1 beta-lactamase mutant I263N in the pres... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i63 | |||||||||
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Title | Crystal structure of TEM1 beta-lactamase mutant I263N in the presence of 1.2 MPa xenon | |||||||||
Components | Beta-lactamase TEM | |||||||||
Keywords | HYDROLASE / xenon | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Roose, B.W. / Dmochowski, I.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Chemphyschem / Year: 2018 Title: A Structural Basis for129Xe Hyper-CEST Signal in TEM-1 beta-Lactamase. Authors: Roose, B.W. / Zemerov, S.D. / Wang, Y. / Kasimova, M.A. / Carnevale, V. / Dmochowski, I.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i63.cif.gz | 398.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i63.ent.gz | 323.9 KB | Display | PDB format |
PDBx/mmJSON format | 5i63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i63_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 5i63_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 5i63_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 5i63_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i63 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i63 | HTTPS FTP |
-Related structure data
Related structure data | 5hviSC 5hw1C 5i52C 5kkfC 5kpuC 6apaC 6aykC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 28912.846 Da / Num. of mol.: 4 / Mutation: M180T, I259N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase #2: Chemical | ChemComp-XE / #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: 2.1 Å3/Da / Density % sol: 41.54 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate (pH 7.0), 20% (w/v) PEG 3350 / PH range: 7.0 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å | |||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.181 Å / Relative weight: 1 | |||||||||||||||
Reflection twin | Operator: h,-k,-l / Fraction: 0.38 | |||||||||||||||
Reflection | Resolution: 1.95→63.36 Å / Num. obs: 68222 / % possible obs: 97.8 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.091 / Rrim(I) all: 0.177 / Net I/σ(I): 7.2 / Num. measured all: 258898 / Scaling rejects: 595 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HVI Resolution: 1.95→60.07 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.1 Å2 / Biso mean: 12.9396 Å2 / Biso min: 1.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→60.07 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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