+Open data
-Basic information
Entry | Database: PDB / ID: 1flz | ||||||
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Title | URACIL DNA GLYCOSYLASE WITH UAAP | ||||||
Components | URACIL-DNA GLYCOSYLASE | ||||||
Keywords | HYDROLASE / glycosylase | ||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Werner, R.M. / Jiang, Y.L. / Gordley, R.G. / Jagadeesh, G.J. / Ladner, J.E. / Xiao, G. / Tordova, M. / Gilliland, G.L. / Stivers, J.T. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase. Authors: Werner, R.M. / Jiang, Y.L. / Gordley, R.G. / Jagadeesh, G.J. / Ladner, J.E. / Xiao, G. / Tordova, M. / Gilliland, G.L. / Stivers, J.T. #1: Journal: Proteins / Year: 1999 Title: Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited Authors: Xiao, G. / Tordova, M. / Jagadeesh, J. / Drohat, A.C. / Stivers, J.T. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1flz.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1flz.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 1flz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1flz_validation.pdf.gz | 383 KB | Display | wwPDB validaton report |
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Full document | 1flz_full_validation.pdf.gz | 415 KB | Display | |
Data in XML | 1flz_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1flz_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/1flz ftp://data.pdbj.org/pub/pdb/validation_reports/fl/1flz | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 25549.910 Da / Num. of mol.: 1 / Mutation: Y19H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Production host: Escherichia coli (E. coli) / References: UniProt: P12295, uridine nucleosidase |
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#2: Chemical | ChemComp-URA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Na HEPES, 2% polyethylene glycol 400, 2.0M ammonium sulfate, 0.002M UAAp, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jun 11, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36 Å / Num. all: 11949 / Num. obs: 11146 / % possible obs: 96 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.26 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 79612 |
-Processing
Software |
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Refinement | Resolution: 2.3→36 Å / Cross valid method: NONE /
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Refinement step | Cycle: LAST / Resolution: 2.3→36 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |