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- PDB-2lzn: Solution structure of S. aureus primase C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2lzn
TitleSolution structure of S. aureus primase C-terminal domain
ComponentsDNA primasePrimase
KeywordsTRANSFERASE / DnaG / primase / helicase / DnaB
Function / homology
Function and homology information


primosome complex / DNA primase activity / DNA helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
DNAb Helicase; Chain A / DNAb Helicase; Chain A / 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 ...DNAb Helicase; Chain A / DNAb Helicase; Chain A / 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 / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / TOPRIM / Toprim domain profile. / TOPRIM domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsShortridge, M.D. / Griep, M.A. / Powers, R.
Citation
Journal: To be Published
Title: Solution structure of S. aureus primase C-terminal domain
Authors: Shortridge, M.D. / Griep, M.A. / Powers, R.
#1: Journal: Biomol.Nmr Assign. / Year: 2012
Title: 1H, 13C, and 15N NMR assignments for the helicase interaction domain of Staphylococcus aureus DnaG primase.
Authors: Shortridge, M.D. / Griep, M.A. / Powers, R.
History
DepositionOct 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,3121
Polymers17,3121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA primase / Primase


Mass: 17311.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: dnaG, SAV1562 / Production host: Escherichia coli (E. coli)
References: UniProt: P63964, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D (H)CCH-COSY
11013D HN(CO)CA
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11413D HNHA

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Sample preparation

DetailsContents: 1.4 mM [U-100% 13C; U-100% 15N] primase CTD, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.4 mM / Component: primase CTD-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 6.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XPLOR-NIHDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1823 / NOE intraresidue total count: 663 / NOE long range total count: 140 / NOE medium range total count: 446 / NOE sequential total count: 460
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 20

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