+Open data
-Basic information
Entry | Database: PDB / ID: 1a96 | ||||||
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Title | XPRTASE FROM E. COLI WITH BOUND CPRPP AND XANTHINE | ||||||
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 / Resolution: 2 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 | 1a96.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a96.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a96_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1a96_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1a96_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 1a96_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a96 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a96 | HTTPS FTP |
-Related structure data
Related structure data | 1a95C 1a97C 1a98C 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
-Protein , 1 types, 4 molecules ABCD
#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) / Cell line: 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 |
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-Non-polymers , 5 types, 150 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 9 Details: XPRT WAS CRYSTALLISED FROM 15 - 20% PEG 4000, 0.1 M AMMONIUM SULPHATE IN 0.1 M BORATE, PH 9., pH 9.0 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 7.6 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: Sep 1, 1997 / 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→100 Å / Num. obs: 45927 / % possible obs: 89.9 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.287 / % possible all: 81.7 |
Reflection | *PLUS Num. measured all: 106769 |
Reflection shell | *PLUS % possible obs: 81.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NUL Resolution: 2→50 Å / Rfactor Rfree error: 0.004 / 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: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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