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Yorodumi- PDB-4jit: Crystal Structure of E. coli XGPRT in complex with (S)-3-(Guanin-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jit | ||||||
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Title | Crystal Structure of E. coli XGPRT in complex with (S)-3-(Guanin-9-yl)pyrrolidin-N-ylacetylphosphonic acid | ||||||
Components | Xanthine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE / PURINE SALVAGE / NUCLEOSIDE PHOSPHONATE / ANTIBACTERIAL | ||||||
Function / homology | Rossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-3ZF / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Keough, D.T. / Hockova, D. / Rejman, D. / Spacek, P. / Vrbkova, S. / Krecmerova, M. / Eng, W.S. / Jans, H. / West, N.P. / Naesens, L.M.J. ...Keough, D.T. / Hockova, D. / Rejman, D. / Spacek, P. / Vrbkova, S. / Krecmerova, M. / Eng, W.S. / Jans, H. / West, N.P. / Naesens, L.M.J. / de Jersey, J. / Guddat, L.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Inhibition of the Escherichia coli 6-oxopurine phosphoribosyltransferases by nucleoside phosphonates: potential for new antibacterial agents. Authors: Keough, D.T. / Hockova, D. / Rejman, D. / Spacek, P. / Vrbkova, S. / Krecmerova, M. / Eng, W.S. / Jans, H. / West, N.P. / Naesens, L.M. / de Jersey, J. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jit.cif.gz | 239 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jit.ent.gz | 196.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jit_validation.pdf.gz | 957.4 KB | Display | wwPDB validaton report |
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Full document | 4jit_full_validation.pdf.gz | 963.3 KB | Display | |
Data in XML | 4jit_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 4jit_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/4jit ftp://data.pdbj.org/pub/pdb/validation_reports/ji/4jit | HTTPS FTP |
-Related 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: 16991.568 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: str. K-12 substr. MDS42 / Gene: gpt, ECMDS42_0227 / Production host: Escherichia coli (E. coli) References: UniProt: H0Q6L9, xanthine phosphoribosyltransferase #2: Chemical | #3: 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: 2.65 Å3/Da / Density % sol: 53.53 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 8% tacsimate, pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 6, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 18634 / Num. obs: 18634 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.8756 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.87 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 29.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.87 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -24.3803 Å / Origin y: 24.8837 Å / Origin z: -2.2408 Å
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Refinement TLS group |
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