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- PDB-7qxm: Crystal structure of the Vibrio cholerae replicative helicase (DnaB) -

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Basic information

Entry
Database: PDB / ID: 7qxm
TitleCrystal structure of the Vibrio cholerae replicative helicase (DnaB)
ComponentsReplicative DNA helicase
KeywordsREPLICATION / Helicase
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding
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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative DNA helicase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLegrand, P. / Quevillon-Cheruel, S. / Walbott, H. / Cargemel, C.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
CitationJournal: Febs Lett. / Year: 2022
Title: The apo-form of the Vibrio cholerae replicative helicase DnaB is a labile and inactive planar trimer of dimers.
Authors: Cargemel, C. / Walbott, H. / Durand, D. / Legrand, P. / Ouldali, M. / Ferat, J.L. / Marsin, S. / Quevillon-Cheruel, S.
History
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase
E: Replicative DNA helicase
F: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)317,6266
Polymers317,6266
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Hexameric Ring
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34540 Å2
ΔGint-171 kcal/mol
Surface area107550 Å2
Unit cell
Length a, b, c (Å)141.230, 150.099, 188.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Replicative DNA helicase


Mass: 52937.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: dnaB, BC353_11625, C9J66_17780, ERS013165_03687, ERS013200_03939, ERS013206_03692, F0315_03560, FLM02_14585, HPY05_12185
Plasmid: pET21
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A085R2T8, DNA helicase

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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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M Sodium Acetate 1.2M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2019 / Details: KB Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.8→32.63 Å / Num. obs: 40084 / % possible obs: 99.9 % / Redundancy: 13.761 % / Biso Wilson estimate: 113.28 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.408 / Rrim(I) all: 0.424 / Χ2: 0.717 / Net I/σ(I): 4.84 / Num. measured all: 551596 / Scaling rejects: 97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.8-3.913.9673.5830.2740854292629250.2413.719100
3.9-4.0114.262.8410.4640412283628340.3122.94699.9
4.01-4.1214.1522.4510.6639428278727860.3982.543100
4.12-4.2514.0351.8521.0237642268326820.5731.922100
4.25-4.3913.7571.4861.3936180263126300.6571.543100
4.39-4.5413.2771.1621.8533869255125510.7661.209100
4.54-4.7113.1070.9662.2432008244224420.7961.005100
4.71-4.9113.9550.8492.6532697234423430.8670.882100
4.91-5.1213.2960.7932.8230181227022700.8750.825100
5.12-5.3713.9610.7663.0230504218521850.8730.795100
5.37-5.6614.5320.7223.3129777204920490.90.748100
5.66-6.0114.4220.663.6828382196819680.9150.684100
6.01-6.4214.230.5454.4926340185118510.9440.565100
6.42-6.9414.0370.4016.1924369173617360.9690.417100
6.94-7.613.6550.2679.2221861160116010.9840.277100
7.6-8.512.810.16613.818561144914490.9930.173100
8.5-9.8112.9450.10620.0316841130113010.9970.111100
9.81-12.0212.7470.0823.9714073110411040.9980.083100
12.02-16.9913.4770.08524.82118738818810.9980.088100
16.99-32.6311.5810.07724.5357445234960.9980.08194.8

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Processing

Software
NameVersionClassification
XSCALEMar 15, 2019data scaling
BUSTER2.10.3 (20-MAY-2020)refinement
PDB_EXTRACT3.27data extraction
XDSMar 15, 2019data reduction
MOLREPVers 11.7.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T66

6t66


Resolution: 3.8→32.63 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.947
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1408 4.84 %RANDOM
Rwork0.2655 ---
obs0.2659 29095 72.7 %-
Displacement parametersBiso max: 263.36 Å2 / Biso mean: 177.98 Å2 / Biso min: 114.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.6164 Å20 Å20 Å2
2--6.782 Å20 Å2
3----4.1657 Å2
Refine analyzeLuzzati coordinate error obs: 0.8 Å
Refinement stepCycle: final / Resolution: 3.8→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20679 0 0 0 20679
Num. residues----2651
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7647SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3638HARMONIC5
X-RAY DIFFRACTIONt_it20975HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2804SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15237SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20975HARMONIC20.004
X-RAY DIFFRACTIONt_angle_deg28363HARMONIC20.61
X-RAY DIFFRACTIONt_omega_torsion1.47
X-RAY DIFFRACTIONt_other_torsion17.52
LS refinement shellResolution: 3.8→3.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3036 31 5.33 %
Rwork0.2333 551 -
all0.2373 582 -
obs--14.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1925-0.08410.28290.43120.03920.1796-0.0014-0.221-0.1050.01240.12730.04450.0967-0.013-0.1259-0.304-0.017-0.0103-0.304-0.1414-0.304-4.668823.12944.4693
20.580.19330.17160-0.23920.0075-0.07510.1535-0.1918-0.01020.0044-0.10570.0935-0.01260.0707-0.27470.0441-0.0118-0.304-0.0868-0.304-3.984420.34173.7447
30.576-0.1618-0.2990.07460.083100.1340.2965-0.0822-0.2583-0.1436-0.02850.2528-0.07780.00970.304-0.0414-0.02580.0595-0.04730.282-1.7575-12.7242-11.0267
40.94470.0307-0.44140.2927-0.22840.435-0.00220.3584-0.1043-0.1569-0.06450.10510.29-0.15610.06670.304-0.0583-0.00440.304-0.1520.304-1.5295-12.2341-11.3715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 174
2X-RAY DIFFRACTION1C13 - 174
3X-RAY DIFFRACTION1E22 - 174
4X-RAY DIFFRACTION2B21 - 174
5X-RAY DIFFRACTION2D22 - 174
6X-RAY DIFFRACTION2F21 - 174
7X-RAY DIFFRACTION3A175 - 461
8X-RAY DIFFRACTION3C175 - 460
9X-RAY DIFFRACTION3E175 - 465
10X-RAY DIFFRACTION4B175 - 460
11X-RAY DIFFRACTION4D175 - 460
12X-RAY DIFFRACTION4F175 - 460

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