+Open data
-Basic information
Entry | Database: PDB / ID: 1nul | ||||||
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Title | XPRTASE FROM E. COLI | ||||||
Components | XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | PHOSPHORIBOSYLTRANSFERASE / TRANSFERASE / PURINE SALVAGE ENZYME | ||||||
Function / homology | Function and homology information xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / Transferases; Glycosyltransferases; Pentosyltransferases ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / Transferases; Glycosyltransferases; Pentosyltransferases / protein homotetramerization / magnesium ion binding / protein-containing complex / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.8 Å | ||||||
Authors | Vos, S. / De Jersey, J. / Martin, J.L. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Crystal structure of Escherichia coli xanthine phosphoribosyltransferase. Authors: Vos, S. / de Jersey, J. / Martin, J.L. #1: Journal: J.Struct.Biol. / Year: 1996 Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Escherichia Coli Xanthine Phosphoribosyltransferase Authors: Vos, S. / De Jersey, J. / Martin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nul.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nul.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nul_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 1nul_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 1nul_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1nul_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/1nul ftp://data.pdbj.org/pub/pdb/validation_reports/nu/1nul | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0901, -0.9906, 0.1028), Vector: |
-Components
#1: Protein | Mass: 16991.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P0A9M5, xanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: 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: 2.15 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: XPRT WAS CRYSTALLISED FROM 18 - 23% PEG 4000, 0.1 M LI2SO4 IN 0.1 M TRIS-HCL, PH 8., pH 8.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→53.2 Å / Num. obs: 25622 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.2 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 77524 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 81.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1644 / Data cutoff low absF: 16.6 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.9 Å / Rfactor Rfree error: 0.019
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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