+Open data
-Basic information
Entry | Database: PDB / ID: 4trb | ||||||
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Title | Sulfolobus solfataricus adenine phosphoribosyltransferase | ||||||
Components | Purine phosphoribosyltransferase (GpT-1) | ||||||
Keywords | TRANSFERASE / Sulfolobus / solfataricus / adenine / phosphoribosyltransferase | ||||||
Function / homology | Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotide binding / PHOSPHATE ION / Purine phosphoribosyltransferase (GpT-1) Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kadziola, A. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Adenine Phosphoribosyltransferase from Sulfolobus solfataricus Is an Enzyme with Unusual Kinetic Properties and a Crystal Structure that Suggests It Evolved from a 6-Oxopurine Phosphoribosyltransferase. Authors: Jensen, K.F. / Hansen, M.R. / Jensen, K.S. / Christoffersen, S. / Poulsen, J.C. / Mlgaard, A. / Kadziola, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4trb.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4trb.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 4trb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/4trb ftp://data.pdbj.org/pub/pdb/validation_reports/tr/4trb | HTTPS FTP |
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-Related structure data
Related structure data | 4trcC 4ts5C 4ts7C 1nulS 1vdmS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 24328.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: gpT-1, SSO2342 / Production host: Escherichia coli (E. coli) References: UniProt: Q97W95, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein: 6.2 mg/mL, 25 mM TRIS pH 7.6, 0.1 mM EDTA, Buffer: 0.1 M MES pH 6.5, Precipitant: 30 % Jeffamine M-600 |
-Data collection
Diffraction | Mean temperature: 122 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 24914 / % possible obs: 100 % / Redundancy: 8.2 % / Net I/σ(I): 23.8 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NUL and 1VDM Resolution: 2.4→19.721 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4 / 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 / Bsol: 52.189 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.721 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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