+Open data
-Basic information
Entry | Database: PDB / ID: 3jt1 | ||||||
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Title | Legionella pneumophila glucosyltransferase Lgt1, UDP-bound form | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | TRANSFERASE / glucosyltransferase / Legionnaire's Disease / Legionella pneumophila | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Lu, W. / Du, J. / Belyi, Y. / Stahl, M. / Zivilikidis, T. / Gerhardt, S. / Aktories, K. / Einsle, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural Basis of the Action of Glucosyltransferase Lgt1 from Legionella pneumophila. Authors: Lu, W. / Du, J. / Stahl, M. / Tzivelekidis, T. / Belyi, Y. / Gerhardt, S. / Aktories, K. / Einsle, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jt1.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jt1.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 3jt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/3jt1 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/3jt1 | HTTPS FTP |
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-Related structure data
Related structure data | 3jszSC 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: 59533.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / Strain: Lens / References: UniProt: Q5WWY0 |
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#2: Chemical | ChemComp-UDP / |
#3: 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: 2.52 Å3/Da / Density % sol: 51.29 % |
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Crystal grow | Temperature: 293.15 K / pH: 5 Details: 1ul protein (4mg/ml) was mixed with 1ul of reservoir solution containing 23% PEG3350, 0.06M ammonium acetat, 0.1M sodium acetate buffer, pH5.0, temperature 293.15K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.8 Å / Num. obs: 26541 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.1 / Num. unique all: 19778 / % possible all: 99.8 |
-Processing
Software | Name: REFMAC / Version: 5.5.0072 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3JSZ Resolution: 2.3→31.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.787 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.249 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→31.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 32.3446 Å / Origin y: -3.7187 Å / Origin z: 32.2563 Å
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