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- PDB-6zns: Crystal Structure of DUF1998 helicase MrfA -

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Basic information

Entry
Database: PDB / ID: 6zns
TitleCrystal Structure of DUF1998 helicase MrfA
ComponentsUncharacterized ATP-dependent helicase YprA
KeywordsHYDROLASE / DNA / REPAIR / HELICASE / MRFA / YPRA / DUF1998
Function / homology
Function and homology information


3'-5' DNA helicase activity / interstrand cross-link repair / nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nucleic acid binding / hydrolase activity / ATP binding
Similarity search - Function
MrfA-like Zn-binding domain / MrfA Zn-binding domain / ATP-dependent helicase HRQ1, winged helix domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily ...MrfA-like Zn-binding domain / MrfA Zn-binding domain / ATP-dependent helicase HRQ1, winged helix domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized ATP-dependent helicase YprA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsRoske, J.J. / Liu, S. / Loll, B. / Neu, U. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG 2473-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: A skipping rope translocation mechanism in a widespread family of DNA repair helicases.
Authors: Roske, J.J. / Liu, S. / Loll, B. / Neu, U. / Wahl, M.C.
History
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4May 1, 2024Group: 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: Uncharacterized ATP-dependent helicase YprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8992
Polymers84,8341
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.943, 191.943, 65.892
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Uncharacterized ATP-dependent helicase YprA


Mass: 84833.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yprA, BSU22220 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: P50830, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl, pH 7.5, 0.2 M MgCl2, 10 % (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.31→50 Å / Num. obs: 13373 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 140.86 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.04
Reflection shellResolution: 3.32→3.52 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2132 / CC1/2: 0.362

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
Cootmodel building
MxCuBEdata collection
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292109739

Resolution: 3.32→47.99 Å / SU ML: 0.9 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 44.7032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3422 669 5 %
Rwork0.3072 12702 -
obs0.309 13371 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128.21 Å2
Refinement stepCycle: LAST / Resolution: 3.32→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 1 0 5057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025150
X-RAY DIFFRACTIONf_angle_d0.52746954
X-RAY DIFFRACTIONf_chiral_restr0.0417784
X-RAY DIFFRACTIONf_plane_restr0.0035892
X-RAY DIFFRACTIONf_dihedral_angle_d16.73761922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.570.52831310.51212497X-RAY DIFFRACTION99.13
3.57-3.930.39471350.36122566X-RAY DIFFRACTION100
3.93-4.50.36321340.31872542X-RAY DIFFRACTION100
4.5-5.660.36131350.30752554X-RAY DIFFRACTION100
5.67-47.990.29261340.26782543X-RAY DIFFRACTION100

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