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Yorodumi- PDB-3i1a: Crystal Structure of apo Spectinomycin Phosphotransferase, APH(9)-Ia -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i1a | ||||||
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Title | Crystal Structure of apo Spectinomycin Phosphotransferase, APH(9)-Ia | ||||||
Components | Spectinomycin phosphotransferase | ||||||
Keywords | TRANSFERASE / protein kinase / aminoglycoside phosphotransferase / antibiotic resistance | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Berghuis, A.M. / Fong, D.H. / Lemke, C.T. / Hwang, J. / Xiong, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure of the antibiotic resistance factor spectinomycin phosphotransferase from Legionella pneumophila. Authors: Fong, D.H. / Lemke, C.T. / Hwang, J. / Xiong, B. / 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 | 3i1a.cif.gz | 172.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i1a.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/3i1a ftp://data.pdbj.org/pub/pdb/validation_reports/i1/3i1a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39644.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: serogroup 1 strain 130b / Gene: aph, aph9 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BB101(DE3) / References: UniProt: O06916 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 200, PEG 3000, aminocaproic acid, DMSO, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.100,0.979462,0.979262,0.95 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2003 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→44.38 Å / Num. all: 135353 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.3 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 7004 / Rsym value: 0.434 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→44.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 271795 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.0236 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→44.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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