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Yorodumi- PDB-4zj3: Crystal structure of cephalexin bound acyl-enzyme intermediate of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zj3 | ||||||
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Title | Crystal structure of cephalexin bound acyl-enzyme intermediate of Val216AcrF mutant TEM1 beta-lactamase from Escherichia coli: E166N and V216AcrF mutant. | ||||||
Components | Beta-lactamase TEM | ||||||
Keywords | HYDROLASE / noncanonical amino acid / beta-lactamase / protein evolution / evolutionary advantage | ||||||
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: 1.7 Å | ||||||
Authors | Xiao, H. / Nasertorabi, F. / Choi, S. / Han, G.W. / Reed, S.A. / Stevens, R.C. / Schultz, P.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Exploring the potential impact of an expanded genetic code on protein function. Authors: Xiao, H. / Nasertorabi, F. / Choi, S.H. / Han, G.W. / Reed, S.A. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zj3.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zj3.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zj3_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 4zj3_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 4zj3_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4zj3_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zj3 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zj3 | HTTPS FTP |
-Related structure data
Related structure data | 4zj1C 4zj2C 1btlS 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: 33328.117 Da / Num. of mol.: 1 / Mutation: E166N,V216AcrF 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase |
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#2: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS USED THE SEQUENCE FROM NCBI REFERENCE SEQUENCE: WP_000027050.1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1M 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.5, 15% PEG 20.000 and 15% PEG 550MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.93 Å / Num. obs: 31711 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BTL Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.323 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / 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: 16.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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