[English] 日本語
Yorodumi- PDB-2mna: The structural basis of DNA binding by the single-stranded DNA-bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mna | ||||||
---|---|---|---|---|---|---|---|
Title | The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN/DNA / DNA repair / SSB / Sulfolobus solfataricus / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information response to ionizing radiation / double-strand break repair via homologous recombination / chromosome / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing, torsion angle dynamics, simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Gamsjaeger, R. / Kariawasam, R. / Gimenez, A.X. / Touma, C.F. / McIlwain, E. / Bernardo, R.E. / Shepherd, N.E. / Ataide, S.F. / Dong, A.Q. / Richard, D.J. ...Gamsjaeger, R. / Kariawasam, R. / Gimenez, A.X. / Touma, C.F. / McIlwain, E. / Bernardo, R.E. / Shepherd, N.E. / Ataide, S.F. / Dong, A.Q. / Richard, D.J. / White, M.F. / Cubeddu, L. | ||||||
Citation | Journal: Biochem.J. / Year: 2015 Title: The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus Authors: Gamsjaeger, R. / Kariawasam, R. / Gimenez, A.X. / Touma, C. / McIlwain, E. / Bernardo, R.E. / Shepherd, N.E. / Ataide, S.F. / Dong, Q. / Richard, D.J. / White, M.F. / Cubeddu, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2mna.cif.gz | 425.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2mna.ent.gz | 356.2 KB | Display | PDB format |
PDBx/mmJSON format | 2mna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mna_validation.pdf.gz | 478.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2mna_full_validation.pdf.gz | 890.9 KB | Display | |
Data in XML | 2mna_validation.xml.gz | 83.4 KB | Display | |
Data in CIF | 2mna_validation.cif.gz | 74.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/2mna ftp://data.pdbj.org/pub/pdb/validation_reports/mn/2mna | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 1780.199 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: Protein | Mass: 12779.369 Da / Num. of mol.: 1 / Fragment: UNP residues 1-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSB, SSO2364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W73 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.8-1.5 mM [U-100% 13C; U-100% 15N] SsoSSB-1, 90 % H2O-2, 10 % D2O-3, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
|
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||
---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics, simulated annealing, torsion angle dynamics, simulated annealing Software ordinal: 1 | ||||||
NMR representative | Selection criteria: lowest energy | ||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10000 / Conformers submitted total number: 10 / Representative conformer: 1 |