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Yorodumi- PDB-1z8s: DnaB binding domain of DnaG (P16) from Bacillus stearothermophilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z8s | ||||||
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Title | DnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597) | ||||||
Components | DNA primase | ||||||
Keywords | TRANSFERASE / two alpha helical sub-domains | ||||||
Function / homology | Function and homology information DNA primase DnaG / DNA primase activity / primosome complex / DNA-directed RNA polymerase complex / DNA helicase activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, cartesian slow-cool annealing energy minimisation | ||||||
Authors | Syson, K. / Thirlway, J. / Hounslow, A.M. / Soultanas, P. / Waltho, J.P. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation Authors: Syson, K. / Thirlway, J. / Hounslow, A.M. / Soultanas, P. / Waltho, J.P. | ||||||
History |
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Remark 999 | SEQUENCE According to authors, residue 530 in the actual sequence is a Glu and 531 is a Leu. The ... SEQUENCE According to authors, residue 530 in the actual sequence is a Glu and 531 is a Leu. The initial sequence submitted in the database for these residues is incorrect. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z8s.cif.gz | 469.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z8s.ent.gz | 389.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z8s_validation.pdf.gz | 344.5 KB | Display | wwPDB validaton report |
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Full document | 1z8s_full_validation.pdf.gz | 512.6 KB | Display | |
Data in XML | 1z8s_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 1z8s_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/1z8s ftp://data.pdbj.org/pub/pdb/validation_reports/z8/1z8s | 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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NMR ensembles |
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-Components
#1: Protein | Mass: 16846.576 Da / Num. of mol.: 1 / Fragment: P16, Residues 451-597 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: dnaG / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9X4D0, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: simultaneously acquired 15N- and 13C-edited 3D NOESY |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, cartesian slow-cool annealing energy minimisation Software ordinal: 1 Details: total of 1707 experimentally determined restraints, 1439 NOE-derived distance constraints, 200 dihedral angle restraints, 68 hydrogen bond distance restraints | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |