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- PDB-1z8s: DnaB binding domain of DnaG (P16) from Bacillus stearothermophilu... -

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Basic information

Entry
Database: PDB / ID: 1z8s
TitleDnaB binding domain of DnaG (P16) from Bacillus stearothermophilus (residues 452-597)
ComponentsDNA primasePrimase
KeywordsTRANSFERASE / two alpha helical sub-domains
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA primase activity / DNA-directed RNA polymerase complex / DNA helicase activity / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Helix Hairpins - #360 / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain ...Helix Hairpins - #360 / DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA Primase, CHC2-type zinc finger / DNA primase, catalytic core, N-terminal domain superfamily / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / Toprim-like / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, cartesian slow-cool annealing energy minimisation
AuthorsSyson, K. / Thirlway, J. / Hounslow, A.M. / Soultanas, P. / Waltho, J.P.
CitationJournal: 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
DepositionMar 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA primase


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA primase / Primase


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: simultaneously acquired 15N- and 13C-edited 3D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM U-15N P1690% H2O/10% D2O
21mM U-15N U13C P1690% H2O/10% D2O
30.5mM U-15N P1650% H2O/50% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM potassium phosphate, 200mM sodium chloride 6.8 ambient 298 K
220mM potassium phosphate, 200mM sodium chloride 6.8 ambient 298 K
320mM potassium phosphate, 200mM sodium chloride 6.8 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Felix2000Accelrys Inc., San Diego, CAprocessing
Felix2000Accelrys Inc., San Diego, CAdata analysis
CNS1.1Brunger, et al.structure solution
CNS1.1Brunger, et al.refinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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