+Open data
-Basic information
Entry | Database: PDB / ID: 1f8x | ||||||
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Title | CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE | ||||||
Components | NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / active site / alpha/beta protein / biocatalyst / nucleoside | ||||||
Function / homology | Function and homology information nucleoside deoxyribosyltransferase / nucleotide salvage / nucleoside deoxyribosyltransferase activity Similarity search - Function | ||||||
Biological species | Lactobacillus leichmannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Armstrong, S.R. / Cook, W.J. / Short, S.A. / Ealick, S.E. | ||||||
Citation | Journal: Structure / Year: 1996 Title: Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site. Authors: Armstrong, S.R. / Cook, W.J. / Short, S.A. / Ealick, S.E. #1: Journal: J.Biol.Chem. / Year: 1990 Title: Crystallization and Preliminary X-ray Investigation of Recombinant Lactobacillus leichmannii Nucleoside Deoxyribosyltransferase Authors: Cook, W.J. / Short, S.A. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f8x.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f8x.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f8x_validation.pdf.gz | 367.6 KB | Display | wwPDB validaton report |
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Full document | 1f8x_full_validation.pdf.gz | 373 KB | Display | |
Data in XML | 1f8x_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1f8x_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f8x ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f8x | HTTPS FTP |
-Related 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: 18098.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lactobacillus leichmannii (bacteria) References: UniProt: Q9R5V5, nucleoside deoxyribosyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.95 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: ammonium sulfate, citrate buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||
Reflection | Resolution: 2.5→100 Å / Num. all: 223078 / Num. obs: 19875 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.115 |
-Processing
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Refinement | Resolution: 2.5→5 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→5 Å
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Refine LS restraints |
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