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- PDB-5guj: Crystal structure of the Bacillus subtilis DnaG RNA Polymerase Do... -

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Basic information

Entry
Database: PDB / ID: 5guj
TitleCrystal structure of the Bacillus subtilis DnaG RNA Polymerase Domain, natural degradation of full length DnaG
ComponentsDNA primase
KeywordsTRANSFERASE
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA helicase activity / DNA-directed RNA polymerase activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria ...DNA primase, catalytic core, N-terminal domain / DNA primase DNAg catalytic core, N-terminal domain / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA primase, catalytic core, N-terminal domain superfamily / : / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA Primase, CHC2-type 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 / Toprim domain profile. / TOPRIM domain / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, Y. / Liu, Z. / Wang, G.
CitationJournal: Sci Rep / Year: 2017
Title: Structural Insight into the Specific DNA Template Binding to DnaG primase in Bacteria
Authors: Zhou, Y. / Luo, H. / Liu, Z. / Yang, M. / Pang, X. / Sun, F. / Wang, G.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)36,9871
Polymers36,9871
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15850 Å2
Unit cell
Length a, b, c (Å)117.114, 117.114, 48.858
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA primase


Mass: 36987.234 Da / Num. of mol.: 1 / Fragment: UNP residues 112-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: dnaG, dnaE, BSU25210 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P05096, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium citrate tribasic dehydrate, 0.1M Tris hydrochloride (pH 8.5) and 30% (w/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.5→29.278 Å / Num. obs: 13480 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4e2k

4e2k


Resolution: 2.5→29.278 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25
RfactorNum. reflection% reflection
Rfree0.2388 606 4.64 %
Rwork0.1885 --
obs0.1908 13069 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 0 76 2678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082651
X-RAY DIFFRACTIONf_angle_d0.8973555
X-RAY DIFFRACTIONf_dihedral_angle_d21.9761607
X-RAY DIFFRACTIONf_chiral_restr0.049384
X-RAY DIFFRACTIONf_plane_restr0.005456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4987-2.750.27591420.21562792X-RAY DIFFRACTION88
2.75-3.14760.31551440.22693189X-RAY DIFFRACTION100
3.1476-3.9640.25871570.18563211X-RAY DIFFRACTION100
3.964-29.28050.18941630.16783271X-RAY DIFFRACTION100

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