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- PDB-6own: Crystal structure of Msm DnaB1 intein splicing domain bound with zinc -

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Basic information

Entry
Database: PDB / ID: 6own
TitleCrystal structure of Msm DnaB1 intein splicing domain bound with zinc
ComponentsReplicative DNA helicase
KeywordsHYDROLASE / Splicing Intein
Function / homology
Function and homology information


primosome complex / intein-mediated protein splicing / DNA replication, synthesis of primer / DNA helicase activity / endonuclease activity / DNA helicase / DNA binding / ATP binding / 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 ...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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBacot-Davis, V.R. / Belfort, M. / Lennon, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5R01GM044844-25 United States
CitationJournal: Mbio / Year: 2020
Title: Conditional DnaB Protein Splicing Is Reversibly Inhibited by Zinc in Mycobacteria.
Authors: Woods, D. / Vangaveti, S. / Egbanum, I. / Sweeney, A.M. / Li, Z. / Bacot-Davis, V. / LeSassier, D.S. / Stanger, M. / Hardison, G.E. / Li, H. / Belfort, M. / Lennon, C.W.
History
DepositionMay 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9758
Polymers43,6483
Non-polymers3275
Water4,702261
1
A: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7464
Polymers14,5491
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6152
Polymers14,5491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Replicative DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6152
Polymers14,5491
Non-polymers651
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

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Components

#1: Protein Replicative DNA helicase


Mass: 14549.445 Da / Num. of mol.: 3 / Fragment: MSM DNAB1 INTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: dnaB, ERS451418_06678 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0D6J385, UniProt: A0R7F4*PLUS, DNA helicase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: MPD, sodium acetate, sodium chloride, and zinc chloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→38.479 Å / Num. obs: 31743 / % possible obs: 99.21 % / Redundancy: 2.8 % / CC1/2: 0.608 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→2.0129 Å / Num. unique obs: 5294 / CC1/2: 0.53 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BS8

6bs8


Resolution: 1.95→38.479 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 1573 4.96 %
Rwork0.2089 30170 -
obs0.2106 31743 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.73 Å2 / Biso mean: 32.7667 Å2 / Biso min: 10.96 Å2
Refinement stepCycle: final / Resolution: 1.95→38.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 5 261 3112
Biso mean--62.58 38.36 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052927
X-RAY DIFFRACTIONf_angle_d0.7634028
X-RAY DIFFRACTIONf_chiral_restr0.055476
X-RAY DIFFRACTIONf_plane_restr0.005535
X-RAY DIFFRACTIONf_dihedral_angle_d2.8191959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.01290.35131420.3213272098
2.0129-2.08490.30291390.2805278099
2.0849-2.16840.29951470.2562277999
2.1684-2.2670.29461490.2386278499
2.267-2.38650.2811380.2311277398
2.3865-2.5360.24771450.2237274798
2.536-2.73180.25511440.2159276898
2.7318-3.00660.22421410.2039273897
3.0066-3.44140.20711420.1857274096
3.4414-4.33490.19511450.1715269794
4.3349-38.4790.25681410.1956264491

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