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- PDB-6znp: Crystal Structure of DUF1998 helicase MrfA bound to DNA -

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Basic information

Entry
Database: PDB / ID: 6znp
TitleCrystal Structure of DUF1998 helicase MrfA bound to DNA
Components
  • Uncharacterized ATP-dependent helicase YprA
  • ssDNADNA
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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 ...MrfA-like Zn-binding domain / MrfA Zn-binding domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
CITRIC ACID / DNA / DNA (> 10) / Uncharacterized ATP-dependent helicase YprA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.16 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized ATP-dependent helicase YprA
B: Uncharacterized ATP-dependent helicase YprA
C: ssDNA
D: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6937
Polymers179,3704
Non-polymers3233
Water181
1
A: Uncharacterized ATP-dependent helicase YprA
C: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9434
Polymers89,6852
Non-polymers2582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized ATP-dependent helicase YprA
D: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7503
Polymers89,6852
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.332, 140.332, 212.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 265 or resid 269...
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLYSA2 - 264
d_12ens_1ILELYSA268 - 568
d_13ens_1ILETHRA572 - 575
d_14ens_1HISPROA584 - 616
d_15ens_1SERGLUA623 - 628
d_16ens_1THRLEUA640 - 641
d_17ens_1LEUILEA644 - 673
d_18ens_1THRTHRA682 - 729
d_19ens_1LYSSERA735 - 748
d_21ens_1LYSSERB1 - 701
d_11ens_2DTDCC
d_21ens_2DTDCD

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.99576811344, 0.0696838148294, 0.0599168607847), (0.0644785847798, 0.994308750628, -0.084809318645), (-0.0654856958447, -0.0805870608414, -0.994594062552)128.037324635, 1.64253878156, 172.749715093
2given(-0.997610499665, 0.0378174521581, 0.0578198172731), (0.0299212751238, 0.990824574243, -0.131800532516), (-0.0622736561652, -0.12975555244, -0.989588544982)133.212005228, 9.06720667857, 179.090298571

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Components

#1: Protein Uncharacterized ATP-dependent helicase YprA


Mass: 84833.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 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: DNA chain ssDNA / DNA


Mass: 4851.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-sodium citrate, 24 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.16→50 Å / Num. obs: 37055 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 60.7 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.9
Reflection shellResolution: 3.16→3.35 Å / Redundancy: 14 % / Num. unique obs: 5841 / CC1/2: 0.411 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
Cootmodel building
MxCuBEdata collection
AutoSolphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.16→19.32 Å / SU ML: 0.441 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2643 1841 5 %
Rwork0.2193 35004 -
obs0.2215 36845 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.95 Å2
Refinement stepCycle: LAST / Resolution: 3.16→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11526 568 15 1 12110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004512400
X-RAY DIFFRACTIONf_angle_d0.726416893
X-RAY DIFFRACTIONf_chiral_restr0.05031906
X-RAY DIFFRACTIONf_plane_restr0.00462083
X-RAY DIFFRACTIONf_dihedral_angle_d18.08681855
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.933998188906
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.917690093316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.240.35271370.33232597X-RAY DIFFRACTION98.59
3.24-3.340.36141400.30732672X-RAY DIFFRACTION100
3.34-3.440.3141400.30262649X-RAY DIFFRACTION99.93
3.44-3.570.3471390.27922641X-RAY DIFFRACTION99.96
3.57-3.710.30091400.24362668X-RAY DIFFRACTION100
3.71-3.880.29731410.23642670X-RAY DIFFRACTION99.96
3.88-4.080.27641400.22812671X-RAY DIFFRACTION100
4.08-4.330.27311410.19742675X-RAY DIFFRACTION100
4.33-4.660.23531410.18372681X-RAY DIFFRACTION100
4.66-5.120.22461430.18112723X-RAY DIFFRACTION99.97
5.12-5.840.25041440.21522731X-RAY DIFFRACTION100
5.85-7.30.25051450.22012756X-RAY DIFFRACTION99.97
7.3-19.320.21191500.18352870X-RAY DIFFRACTION99.44

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