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Yorodumi- PDB-4qy5: Crystal structures of chimeric beta-lactamase cTEM-19m showing di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qy5 | ||||||
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Title | Crystal structures of chimeric beta-lactamase cTEM-19m showing different conformations | ||||||
Components | Beta-lactamase TEM,Beta-lactamase PSE-4 | ||||||
Keywords | HYDROLASE | ||||||
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) Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å | ||||||
Authors | Park, J. / Gobeil, S. / Pelletier, J.N. / Berghuis, A.M. | ||||||
Citation | Journal: To be Published Title: Crystal structures of chimeric beta-lactamase cTEM-19m showing different conformations Authors: Park, J. / Gobeil, S. / Pelletier, J.N. / Berghuis, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qy5.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qy5.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qy5_validation.pdf.gz | 409.5 KB | Display | wwPDB validaton report |
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Full document | 4qy5_full_validation.pdf.gz | 409.7 KB | Display | |
Data in XML | 4qy5_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4qy5_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/4qy5 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qy5 | HTTPS FTP |
-Related structure data
Related structure data | 4qy6C 4zg4S 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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Unit cell |
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-Components
#1: Protein | Mass: 28827.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6, pse4, carB1 / Production host: Escherichia coli (E. coli) References: UniProt: P62593, UniProt: P16897, beta-lactamase | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | #4: 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: 2.02 Å3/Da / Density % sol: 39.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG 4000, 0.2M magnesium chloride, 0.1M TrisHCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 12, 2011 |
Radiation | Monochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.4 Å / Num. all: 38195 / Num. obs: 38195 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2767 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ZG4 Resolution: 1.501→51.4 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.834 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.064 / 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: 18.022 Å2
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Refinement step | Cycle: LAST / Resolution: 1.501→51.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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