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Yorodumi- PDB-4zj1: Crystal Structure of p-acrylamido-phenylalanine modified TEM1 bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zj1 | ||||||
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Title | Crystal Structure of p-acrylamido-phenylalanine modified TEM1 beta-lactamase from Escherichia coli : 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 / MOLECULAR REPLACEMENT / Resolution: 1.54 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 | 4zj1.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zj1.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zj1_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 4zj1_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 4zj1_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4zj1_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zj1 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zj1 | HTTPS FTP |
-Related structure data
Related structure data | 4zj2C 4zj3C 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: 32995.734 Da / Num. of mol.: 1 / Mutation: 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: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-MES / |
#4: Chemical | ChemComp-PEG / |
#5: 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: 2.09 Å3/Da / Density % sol: 41.11 % |
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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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→26.54 Å / Num. obs: 41549 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.54→1.63 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BTL Resolution: 1.54→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.077 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / 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: 16.414 Å2
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Refinement step | Cycle: 1 / Resolution: 1.54→25 Å
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Refine LS restraints |
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