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Yorodumi- PDB-3uzr: Crystal structure of aminoglycoside phosphotransferase APH(2'')-I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uzr | |||||||||
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Title | Crystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, apo form | |||||||||
Components | Aminoglycoside phosphotransferase | |||||||||
Keywords | TRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / aminoglycoside phosphotransferase / antibiotic resistance / cytoplasmic / intracellular | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | |||||||||
Authors | Stogios, P.J. / Minasov, G. / Singer, A.U. / Tan, K. / Nocek, B. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of aminoglycoside phosphotransferase APH(2'')-Ib, apo form Authors: Stogios, P.J. / Minasov, G. / Singer, A.U. / Tan, K. / Nocek, B. / Evdokimova, E. / Egorova, E. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uzr.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uzr.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 3uzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/3uzr ftp://data.pdbj.org/pub/pdb/validation_reports/uz/3uzr | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38155.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aph(2')-Ib / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93ET9 |
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-Non-polymers , 5 types, 268 molecules
#2: Chemical | ChemComp-MG / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-PG4 / | #6: 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: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M MG CHLORIDE, 0.1 M HEPES PH 7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 24877 / Num. obs: 25410 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.086 / Net I/σ(I): 23.28 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.61 / Rsym value: 0.391 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→19.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.46 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.181 / 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: 29.454 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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