+Open data
-Basic information
Entry | Database: PDB / ID: 4gku | ||||||
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Title | Crystal structure of beta lactamase in PET-15B | ||||||
Components | Beta-lactamase TEM | ||||||
Keywords | HYDROLASE / beta lactamase | ||||||
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: 1.915 Å | ||||||
Authors | Zhang, Y. / Cao, C. | ||||||
Citation | Journal: To be published Title: Crystal structure of beta lactamase in PET-15B Authors: Zhang, Y. / Cao, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gku.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gku.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/4gku ftp://data.pdbj.org/pub/pdb/validation_reports/gk/4gku | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28941.994 Da / Num. of mol.: 1 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.2M magnesium chloride, 0.1M BIS-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.2605 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2605 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 37743 / Num. obs: 37743 / % possible obs: 98.1 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 100.8 / Redundancy: 13.1 % |
Reflection shell | Resolution: 1.91→1.98 Å / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.915→34.917 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.915→34.917 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: 10
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