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- PDB-6bs8: The class 3 DnaB intein from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6bs8
TitleThe class 3 DnaB intein from Mycobacterium smegmatis
ComponentsReplicative DNA helicase
KeywordsHYDROLASE / class 3 intein / DnaB
Function / homology
Function and homology information


DNA 5'-3' helicase / intein-mediated protein splicing / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / endonuclease activity / DNA helicase / ATP hydrolysis activity / DNA binding ...DNA 5'-3' helicase / intein-mediated protein splicing / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / endonuclease activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / cytosol / cytoplasm
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 / LAGLIDADG-like domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / Intein splicing domain ...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 / LAGLIDADG-like domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative DNA helicase / Replicative DNA helicase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLi, Z. / Kelley, D.S. / Banavali, N. / Belfort, M. / Li, H.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM39422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM44844 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI055429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Nat Commun / Year: 2018
Title: Mycobacterial DnaB helicase intein as oxidative stress sensor.
Authors: Kelley, D.S. / Lennon, C.W. / Li, Z. / Miller, M.R. / Banavali, N.K. / Li, H. / Belfort, M.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)43,6483
Polymers43,6483
Non-polymers00
Water5,459303
1
A: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)14,5491
Polymers14,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)14,5491
Polymers14,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)14,5491
Polymers14,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.050, 56.914, 64.727
Angle α, β, γ (deg.)90.000, 106.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 34 or resid 36...
21(chain B and (resid 1 through 34 or resid 36...
31(chain C and (resid 1 through 34 or resid 36...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHR(chain A and (resid 1 through 34 or resid 36...AA1 - 341 - 34
12VALVALGLYGLY(chain A and (resid 1 through 34 or resid 36...AA36 - 4536 - 45
13PROPROALAALA(chain A and (resid 1 through 34 or resid 36...AA47 - 6347 - 63
14HISHISLEULEU(chain A and (resid 1 through 34 or resid 36...AA65 - 7965 - 79
15ALAALAVALVAL(chain A and (resid 1 through 34 or resid 36...AA81 - 8781 - 87
16VALVALARGARG(chain A and (resid 1 through 34 or resid 36...AA103 - 109103 - 109
17PROPROARGARG(chain A and (resid 1 through 34 or resid 36...AA112 - 117112 - 117
18VALVALPROPRO(chain A and (resid 1 through 34 or resid 36...AA119 - 124119 - 124
19HISHISASNASN(chain A and (resid 1 through 34 or resid 36...AA126 - 139126 - 139
21ALAALATHRTHR(chain B and (resid 1 through 34 or resid 36...BB1 - 341 - 34
22VALVALGLYGLY(chain B and (resid 1 through 34 or resid 36...BB36 - 4536 - 45
23PROPROALAALA(chain B and (resid 1 through 34 or resid 36...BB47 - 6347 - 63
24HISHISLEULEU(chain B and (resid 1 through 34 or resid 36...BB65 - 7965 - 79
25ALAALAVALVAL(chain B and (resid 1 through 34 or resid 36...BB81 - 8781 - 87
26VALVALARGARG(chain B and (resid 1 through 34 or resid 36...BB103 - 109103 - 109
27PROPROARGARG(chain B and (resid 1 through 34 or resid 36...BB112 - 117112 - 117
28VALVALPROPRO(chain B and (resid 1 through 34 or resid 36...BB119 - 124119 - 124
29HISHISASNASN(chain B and (resid 1 through 34 or resid 36...BB126 - 139126 - 139
31ALAALATHRTHR(chain C and (resid 1 through 34 or resid 36...CC1 - 341 - 34
32VALVALGLYGLY(chain C and (resid 1 through 34 or resid 36...CC36 - 4536 - 45
33PROPROALAALA(chain C and (resid 1 through 34 or resid 36...CC47 - 6347 - 63
34HISHISLEULEU(chain C and (resid 1 through 34 or resid 36...CC65 - 7965 - 79
35ALAALAVALVAL(chain C and (resid 1 through 34 or resid 36...CC81 - 8781 - 87
36VALVALARGARG(chain C and (resid 1 through 34 or resid 36...CC103 - 109103 - 109
37PROPROARGARG(chain C and (resid 1 through 34 or resid 36...CC112 - 117112 - 117
38VALVALPROPRO(chain C and (resid 1 through 34 or resid 36...CC119 - 124119 - 124
39HISHISASNASN(chain C and (resid 1 through 34 or resid 36...CC126 - 139126 - 139

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Components

#1: Protein Replicative DNA helicase


Mass: 14549.445 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: dnaB, ERS451418_06678 / Plasmid: pXI / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6J385, UniProt: I7FPC4*PLUS, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.6
Details: 20% (v/v) 2-Methyl-2,4-pentanediol (MPD), 0.1 M sodium acetate, pH 4.6, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. obs: 31802 / % possible obs: 97 % / Redundancy: 2.7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.066 / Rrim(I) all: 0.116 / Χ2: 1.817 / Net I/av σ(I): 11.9 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.982.30.7822.115680.6040.6030.9931.5197.6
1.98-2.022.40.72416240.6690.5420.9091.54898.5
2.02-2.062.50.62415790.6960.4580.7781.46898.8
2.06-2.12.60.58516370.7550.4170.7221.65498.7
2.1-2.152.70.49216170.8010.3450.6031.54599
2.15-2.22.70.43215940.850.2990.5281.65698.9
2.2-2.252.70.39216090.8750.2710.4791.70799
2.25-2.312.70.35216190.9020.2430.431.72998.1
2.31-2.382.70.28215990.9290.1910.3421.6698.2
2.38-2.462.70.27416070.9240.1880.3341.75498.3
2.46-2.542.70.23415630.9320.1590.2841.74698.1
2.54-2.652.70.1916280.960.1290.2311.80298.3
2.65-2.772.70.15116080.9710.1020.1831.98897.8
2.77-2.912.70.12515870.9740.0850.1521.96597.4
2.91-3.12.80.09415980.9870.0640.1142.09296.6
3.1-3.332.80.06815660.9910.0460.0831.98995.3
3.33-3.672.80.05615580.9920.0380.0682.07495.5
3.67-4.22.80.04615510.9950.0310.0562.28393.7
4.2-5.292.90.03615600.9960.0240.0431.95793
5.29-1002.90.03415300.9970.0230.0411.95289.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.95→38.48 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76
RfactorNum. reflection% reflection
Rfree0.2354 1574 4.96 %
Rwork0.2025 --
obs0.2041 31746 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.38 Å2 / Biso mean: 32.2391 Å2 / Biso min: 3.58 Å2
Refinement stepCycle: final / Resolution: 1.95→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 0 303 3149
Biso mean---39.35 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082934
X-RAY DIFFRACTIONf_angle_d0.9914039
X-RAY DIFFRACTIONf_chiral_restr0.065477
X-RAY DIFFRACTIONf_plane_restr0.007537
X-RAY DIFFRACTIONf_dihedral_angle_d3.7751963
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1511X-RAY DIFFRACTION11.406TORSIONAL
12B1511X-RAY DIFFRACTION11.406TORSIONAL
13C1511X-RAY DIFFRACTION11.406TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.0130.32781420.29772720286298
2.013-2.08490.27621400.26712781292199
2.0849-2.16840.29031470.24232779292699
2.1684-2.26710.28181490.23142787293699
2.2671-2.38660.28631380.2282772291098
2.3866-2.53610.24421450.21492746289198
2.5361-2.73180.25051440.21022768291298
2.7318-3.00670.20881410.19662738287997
3.0067-3.44150.18761420.18152741288396
3.4415-4.3350.20131450.16782696284194
4.335-38.48770.24061410.18682644278591

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