+Open data
-Basic information
Entry | Database: PDB / ID: 2ru8 | ||||||
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Title | DnaT C-terminal domain | ||||||
Components | Primosomal protein 1 | ||||||
Keywords | REPLICATION / Primosome / replication restart / DnaT / DNA binding | ||||||
Function / homology | Function and homology information DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / DNA replication, synthesis of primer / replication fork processing / DNA unwinding involved in DNA replication / protein homotrimerization / DNA-templated DNA replication / single-stranded DNA binding / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Abe, Y. / Tani, J. / Fujiyama, S. / Urabe, M. / Sato, K. / Aramaki, T. / Katayama, T. / Ueda, T. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Structure and mechanism of the primosome protein DnaT-functional structures for homotrimerization, dissociation of ssDNA from the PriB·ssDNA complex, and formation of the DnaT·ssDNA complex. Authors: Fujiyama, S. / Abe, Y. / Tani, J. / Urabe, M. / Sato, K. / Aramaki, T. / Katayama, T. / Ueda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ru8.cif.gz | 561.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ru8.ent.gz | 473.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ru8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/2ru8 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/2ru8 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11237.618 Da / Num. of mol.: 1 / Fragment: ssDNA binding domain, UNP residues 89-179 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8J2 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 752 / NOE intraresidue total count: 251 / NOE long range total count: 101 / NOE medium range total count: 157 / NOE sequential total count: 243 / Hydrogen bond constraints total count: 26 / Protein phi angle constraints total count: 55 / Protein psi angle constraints total count: 55 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |