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Yorodumi- PDB-1syf: ENGINEERING ALTERNATIVE BETA-TURN TYPES IN STAPHYLOCOCCAL NUCLEASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1syf | ||||||
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Title | ENGINEERING ALTERNATIVE BETA-TURN TYPES IN 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Hynes, T.R. / Hodel, A. / Fox, R.O. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Engineering alternative beta-turn types in staphylococcal nuclease. Authors: Hynes, T.R. / Hodel, A. / Fox, R.O. #1: Journal: Proteins / Year: 1991 Title: The Crystal Structure of Staphylococcal Nuclease Refined at 1.7 Angstroms Resolution Authors: Hynes, T.R. / Fox, R.O. #2: Journal: Nature / Year: 1989 Title: Transfer of a Beta-Turn Structure to a New Protein Context Authors: Hynes, T.R. / Kautz, R.A. / Goodman, M.A. / Gill, J.F. / Fox, R.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1syf.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1syf.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1syf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1syf_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 1syf_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 1syf_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1syf_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/1syf ftp://data.pdbj.org/pub/pdb/validation_reports/sy/1syf | 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: 16847.318 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: 2.22 Å3/Da / Density % sol: 44.49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 5 ℃ / pH: 8.15 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. obs: 13515 / % possible obs: 100 % / Num. measured all: 99105 / Rmerge(I) obs: 0.072 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→8 Å / Rfactor obs: 0.168 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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