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- PDB-4zc0: Structure of a dodecameric bacterial helicase -

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Basic information

Entry
Database: PDB / ID: 4zc0
TitleStructure of a dodecameric bacterial helicase
ComponentsReplicative DNA helicase
KeywordsHYDROLASE / Helicase ATPase DNA replication / dodecamer
Function / homology
Function and homology information


DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / isomerase activity / 5'-3' DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding ...DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / isomerase activity / 5'-3' DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA helicase, DnaB type / 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 / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 6.7 Å
AuthorsBazin, A. / Cherrier, M.V. / Gutsche, I. / Timmins, J. / Terradot, L.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure and primase-mediated activation of a bacterial dodecameric replicative helicase.
Authors: Bazin, A. / Cherrier, M.V. / Gutsche, I. / Timmins, J. / Terradot, L.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,4075
Polymers238,3624
Non-polymers2,0451
Water00
1
A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
hetero molecules

A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
hetero molecules

A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)721,22115
Polymers715,08712
Non-polymers6,1343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)283.467, 283.467, 283.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein
Replicative DNA helicase


Mass: 59590.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: dnaB, HP_1362 / Production host: Escherichia coli (E. coli) / References: UniProt: O25916, DNA helicase
#2: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6

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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: 3.98 Å3/Da / Density % sol: 69.11 % / Description: Cubic
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Polyethylene glycol 3350 26%, 100 mM Tris pH 8.6 and 200 mM Lithium Sulphate
PH range: 8

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.2546 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2546 Å / Relative weight: 1
ReflectionResolution: 6.7→48.61 Å / Num. obs: 6960 / % possible obs: 99.7 % / Redundancy: 44.3 % / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / Net I/σ(I): 18.3
Reflection shellResolution: 6.7→7.06 Å / Redundancy: 45.6 % / Rmerge(I) obs: 4.725 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 6.7→47.245 Å / SU ML: 1.08 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 34.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2988 685 5.19 %Random selection
Rwork0.2577 ---
obs0.2597 13211 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.7→47.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9131 0 18 0 9149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049291
X-RAY DIFFRACTIONf_angle_d0.83812650
X-RAY DIFFRACTIONf_dihedral_angle_d17.7383842
X-RAY DIFFRACTIONf_chiral_restr0.0331430
X-RAY DIFFRACTIONf_plane_restr0.0031631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.7-7.21570.34941520.31452526X-RAY DIFFRACTION100
7.2157-7.93870.35171230.27342479X-RAY DIFFRACTION100
7.9387-9.08040.32451330.20872513X-RAY DIFFRACTION100
9.0804-11.41360.26921490.20092482X-RAY DIFFRACTION100
11.4136-47.24570.29831280.3022526X-RAY DIFFRACTION100

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