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Yorodumi- PDB-1sty: THE ALPHA ANEURISM: A STRUCTURAL MOTIF REVEALED IN AN INSERTION M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sty | ||||||
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Title | THE ALPHA ANEURISM: A STRUCTURAL MOTIF REVEALED IN AN INSERTION MUTANT OF STAPHYLOCOCCAL NUCLEASE | ||||||
Components | STAPHYLOCOCCAL NUCLEASE | ||||||
Keywords | HYDROLASE (PHOSPHORIC DIESTER) | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.67 Å | ||||||
Authors | Keefe, L.J. / Lattman, E.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease. Authors: Keefe, L.J. / Sondek, J. / Shortle, D. / Lattman, E.E. #1: Journal: J.Appl.Crystallogr. / Year: 1992 Title: Resolution of a Protein Sequence Ambiguity by X-Ray Crystallographic and Mass Spectrometric Methods Authors: Keefe, L.J. / Lattman, E.E. / Wolkow, C. / Woods, A. / Chevrier, M. / Cotter, R.J. | ||||||
History |
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Remark 650 | HELIX THE ALPHA ANEURISM IS A UNIQUE BULGE IN AN ALPHA HELIX WHICH OCCURS AT THE INSERTION SITE OF ...HELIX THE ALPHA ANEURISM IS A UNIQUE BULGE IN AN ALPHA HELIX WHICH OCCURS AT THE INSERTION SITE OF THE GLYCINE RESIDUE (IN THE C-TERMINAL ALPHA HELIX BETWEEN RESIDUES ARG 126 AND LYS 127). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sty.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sty.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sty_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 1sty_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 1sty_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 1sty_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/1sty ftp://data.pdbj.org/pub/pdb/validation_reports/st/1sty | 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 | 2: RESIDUE PRO 117 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 16900.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00644, micrococcal nuclease |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-THP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.01 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 7 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.67 Å / Num. obs: 13012 / % possible obs: 87.8 % / Observed criterion σ(F): 2 / Num. measured all: 42377 / Rmerge(I) obs: 0.0502 |
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-Processing
Software |
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Refinement | Rfactor Rwork: 0.17 / Highest resolution: 1.67 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.67 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR/PROLSQ / Classification: refinement | |||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / Rfactor Rwork: 0.17 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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