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Yorodumi- PDB-4dj4: X-ray structure of mutant N211D of bifunctional nuclease TBN1 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dj4 | |||||||||
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Title | X-ray structure of mutant N211D of bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato) | |||||||||
Components | Nuclease | |||||||||
Keywords | HYDROLASE / mainly alpha helical / trinuclear metal centre / bi-functional / nuclease / 3'-nucleotidase / cytosol membrane associated | |||||||||
Function / homology | Function and homology information Aspergillus nuclease S1 / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA endonuclease activity / nucleic acid binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Koval, T. / Stepankova, A. / Lipovova, P. / Podzimek, T. / Matousek, J. / Duskova, J. / Skalova, T. / Hasek, J. / Dohnalek, J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. Authors: Koval, T. / Lipovova, P. / Podzimek, T. / Matousek, J. / Duskova, J. / Skalova, T. / Stepankova, A. / Hasek, J. / Dohnalek, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dj4.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dj4.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 4dj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dj4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4dj4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4dj4_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4dj4_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/4dj4 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4dj4 | HTTPS FTP |
-Related structure data
Related structure data | 3sngSC 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, 2 molecules AB
#1: Protein | Mass: 31647.520 Da / Num. of mol.: 2 / Mutation: N211D Source method: isolated from a genetically manipulated source Details: pLV07 is a derivative of plant binary vector pBinPLUS; TBN1 cDNA sequence is driven from 35S promoter of CaMV, and terminated by CaMV terminator. Expression casette is placed between left ...Details: pLV07 is a derivative of plant binary vector pBinPLUS; TBN1 cDNA sequence is driven from 35S promoter of CaMV, and terminated by CaMV terminator. Expression casette is placed between left and right borders of T-DNA. Source: (gene. exp.) Solanum lycopersicum (tomato) / Strain: cv. Rutgers / Gene: tbn1 / Plasmid: pLV07 / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q0KFV0 |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 178 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | #7: Chemical | ChemComp-NA / | #8: 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: 2.7 Å3/Da / Density % sol: 54.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.16 M Magnesium chloride 0.08 M TRIS pH 8.5 19% w/v Polyethylene glycol 3,350 3.3% Butane-1,4-diol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2010 / Details: 2 mirrors and a double-crystal monochromator |
Radiation | Monochromator: KMC-1, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→35 Å / Num. obs: 26874 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 5.7 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1524 / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SNG Resolution: 2.35→35 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 4.736 / SU ML: 0.115 / Isotropic thermal model: isotropic / Cross valid method: Rfree throughout / σ(F): 0 / ESU R: 0.324 Stereochemistry target values: CCP4 stereochemistry library, version 6.2.0 Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT. THE LAST STEPS OF REFINEMENT OF THIS STRUCTURE WERE DONE USING ALL REFLECTIONS. CALCULATION OF THE REPORTED VALUES OF RWORK AND ...Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT. THE LAST STEPS OF REFINEMENT OF THIS STRUCTURE WERE DONE USING ALL REFLECTIONS. CALCULATION OF THE REPORTED VALUES OF RWORK AND RFREE PRECEDED THIS LAST STEP OF REFINEMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.612 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.352→2.413 Å / Total num. of bins used: 20
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