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Yorodumi- PDB-4mej: Crystal structure of Lactobacillus helveticus purine deoxyribosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mej | ||||||
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Title | Crystal structure of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine) | ||||||
Components | Nucleoside deoxyribosyltransferase | ||||||
Keywords | transferase/transferase inhibitor / purine deoxyribosyl transferase (PDT) / transferase-transferase inhibitor complex | ||||||
Function / homology | Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / transferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 3H-imidazo[2,1-b]purin-4(5H)-one / Nucleoside deoxyribosyltransferase Function and homology information | ||||||
Biological species | Lactobacillus helveticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Paul, D. / Seckute, J. / Ealick, S.E. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Glycosylation of a tricyclic purine analog at alternative sites by nucleoside 2 -deoxyribosyltransferases Authors: Ye, W. / Paul, D. / Gao, L. / Seckute, J. / Sangaiah, R. / Karupiah, J. / Zhang, Z. / Kaminski, A.P. / Ealick, S.E. / Gold, A. / Ball, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mej.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mej.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/4mej ftp://data.pdbj.org/pub/pdb/validation_reports/me/4mej | HTTPS FTP |
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-Related structure data
Related structure data | 1s2lS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: (Selection details: chain 'C' RESTRAINED TORSIONS: 2342 Histogram of differences under limit:...) |
-Components
#1: Protein | Mass: 18733.189 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus helveticus (bacteria) / Strain: H10 / Gene: LBHH_1694 / Production host: Escherichia coli (E. coli) / References: UniProt: F0NW64 #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: 2.64 Å3/Da / Density % sol: 53.36 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 100 mM Tris and 2.2 M ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2007 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 35578 / Num. obs: 35578 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.049 / Rsym value: 0.046 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3279 / Rsym value: 0.266 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1S2L Resolution: 2.1→36.648 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→36.648 Å
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Refine LS restraints |
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LS refinement shell |
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