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Yorodumi- PDB-3dni: CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dni | |||||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF DNASE I AT 2 ANGSTROMS RESOLUTION | |||||||||
Components | DEOXYRIBONUCLEASE I | |||||||||
Keywords | ENDONUCLEASE | |||||||||
Function / homology | Function and homology information regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / neutrophil activation involved in immune response / deoxyribonuclease I activity / DNA catabolic process / nuclear envelope / actin binding / apoptotic process ...regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / neutrophil activation involved in immune response / deoxyribonuclease I activity / DNA catabolic process / nuclear envelope / actin binding / apoptotic process / DNA binding / extracellular region / nucleus Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Oefner, C. / Suck, D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1986 Title: Crystallographic refinement and structure of DNase I at 2 A resolution. Authors: Oefner, C. / Suck, D. #1: Journal: J.Mol.Biol. / Year: 1992 Title: X-Ray Structure of the DNase I-D(Ggtatacc)2 Complex at 2.3 Angstroms Resolution Authors: Weston, S.A. / Lahm, A. / Suck, D. #2: Journal: J.Mol.Biol. / Year: 1991 Title: DNase I-Induced DNA Conformation. 2 Angstroms Structure of a DNase I-Octamer Complex Authors: Lahm, A. / Suck, D. #3: Journal: Nature / Year: 1988 Title: Structure Refined to 2 Angstroms of a Nicked DNA Octanucleotide Complex with DNase I Authors: Suck, D. / Lahm, A. / Oefner, C. #4: Journal: Nature / Year: 1986 Title: Structure of DNase I at 2.0 Angstroms Resolution Suggests a Mechanism for Binding to and Cutting DNA Authors: Suck, D. / Oefner, C. #5: Journal: Embo J. / Year: 1984 Title: Three-Dimensional Structure of Bovine Pancreatic DNase I at 2.5 Angstroms Resolution Authors: Suck, D. / Oefner, C. / Kabsch, W. #6: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallization and Preliminary Crystallographic Data of Bovine Pancreatic Deoxyribonuclease I Authors: Suck, D. #7: Journal: J.Biol.Chem. / Year: 1973 Title: Bovine Pancreatic Deoxyribonucleasea. Isolation of Cyanogen Bromide Peptides, Complete Covalent Structure of the Polypeptide Chain Authors: Liao, T.-H. / Salnikow, J. / Moore, S. / Stein, W.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dni.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dni.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dni_validation.pdf.gz | 483 KB | Display | wwPDB validaton report |
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Full document | 3dni_full_validation.pdf.gz | 500.1 KB | Display | |
Data in XML | 3dni_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3dni_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dni ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dni | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: OF THE CARBOHYDRATE MOIETY ATTACHED TO ASN 18, 7 RESIDUES HAVE BEEN REFINED AND INCLUDED IN THE ENTRY. THE CARBOHYDRATE MOIETY IS ARRANGED AS FOLLOWS: MAN (264) - MAN (265) / N18 - NAG(261) - ...1: OF THE CARBOHYDRATE MOIETY ATTACHED TO ASN 18, 7 RESIDUES HAVE BEEN REFINED AND INCLUDED IN THE ENTRY. THE CARBOHYDRATE MOIETY IS ARRANGED AS FOLLOWS: MAN (264) - MAN (265) / N18 - NAG(261) - NAG(262) - MAN(263) \ MAN (266) - MAN (267) WHERE MAN (263) - MAN (264) IS LINKED 1-6 MAN (263) - MAN (266) IS LINKED 1-4 |
-Components
#1: Protein | Mass: 29092.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: pancreas / References: UniProt: P00639, deoxyribonuclease I | ||
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#2: Polysaccharide | alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]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 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 19 ℃ / pH: 6.6 / Method: unknown / Details: referred to J.Mol.Biol. 162.511-513 1982 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.5 Å / Num. obs: 9025 / % possible obs: 86 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.064 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→6 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection all: 17774 / σ(F): 0 / Rfactor all: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |