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Yorodumi- PDB-1sta: ACCOMMODATION OF INSERTION MUTATIONS ON THE SURFACE AND IN THE IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sta | ||||||
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Title | ACCOMMODATION OF INSERTION MUTATIONS ON THE SURFACE AND IN THE INTERIOR 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: 1.7 Å | ||||||
Authors | Keefe, L.J. / Quirk, S. / Gittis, A. / Lattman, E.E. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease. Authors: Keefe, L.J. / Quirk, S. / Gittis, A. / Sondek, J. / Lattman, E.E. #1: 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. | ||||||
History |
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Remark 700 | SHEET THE TWO INSERTED GLYCINE RESIDUES ARE ACCOMMODATED IN A SPECIAL THREE-RESIDUE BETA-BULGE. A ...SHEET THE TWO INSERTED GLYCINE RESIDUES ARE ACCOMMODATED IN A SPECIAL THREE-RESIDUE BETA-BULGE. A BRIDGING WATER MOLECULE IN THE NEWLY CREATED CAVITY SATISFIES THE HYDROGEN BONDING REQUIREMENTS OF THE BETA-SHEET BY FORMING A BIFURCATED HYDROGEN BOND TO TWO BACKBONE CARBONYL GROUPS ON ONE BETA-STRAND AND BY FORMING A SINGLE HYDROGEN BOND TO THE BACKBONE AMIDE GROUP ON THE OTHER BETA-STRAND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sta.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sta.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sta_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 1sta_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 1sta_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1sta_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/1sta ftp://data.pdbj.org/pub/pdb/validation_reports/st/1sta | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 117 |
-Components
#1: Protein | Mass: 16957.436 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: 2.13 Å3/Da / Density % sol: 42.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.15 / Method: vapor diffusionDetails: taken from Loll, P.J. and Lattman, E.E. (1989). Proteins Struct. Funct. Genet., 5, 183-201. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software |
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Refinement | Resolution: 1.7→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.182 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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