+Open data
-Basic information
Entry | Database: PDB / ID: 1a98 | ||||||
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Title | XPRTASE FROM E. COLI COMPLEXED WITH GMP | ||||||
Components | XANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | PHOSPHORIBOSYLTRANSFERASE / TRANSFERASE / PURINE SALVAGE ENZYME / GLYCOSYLTRANSFERASE | ||||||
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 / MOLECULAR REPLACEMENT MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Vos, S. / Parry, R.J. / Burns, M.R. / De Jersey, J. / Martin, J.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase. Authors: Vos, S. / Parry, R.J. / Burns, M.R. / 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 | 1a98.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a98.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a98_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 1a98_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 1a98_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1a98_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a98 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a98 | HTTPS FTP |
-Related structure data
Related structure data | 1a95C 1a96C 1a97C 1nulS 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: 16959.502 Da / Num. of mol.: 2 / Mutation: C59A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Cellular location: CYTOPLASM / Gene: GPT / Plasmid: PT7-7 / Cellular location (production host): CYTOPLASM / Culture collection (production host): ATCC 87050 / Gene (production host): GPT / Production host: Escherichia coli (E. coli) / Strain (production host): SPHI606 References: UniProt: P0A9M5, xanthine phosphoribosyltransferase #2: 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 CRYSTALLIZED FROM 20% PEG4000 IN 0.1 M TRIS-HCL, pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / 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 RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 29, 1994 / 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: 2.25→60 Å / Num. obs: 11089 / % possible obs: 79.5 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.172 / % possible all: 66.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 16902 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 66.9 % / Rmerge(I) obs: 0.172 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NUL Resolution: 2.25→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 36.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.326 / Rfactor Rwork: 0.308 |