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- PDB-6znq: Crystal Structure of DUF1998 helicase MrfA bound to DNA and AMPPNP -

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Basic information

Entry
Database: PDB / ID: 6znq
TitleCrystal Structure of DUF1998 helicase MrfA bound to DNA and AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CITRIC ACID / DNA / DNA (> 10) / Uncharacterized ATP-dependent helicase YprA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 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

Downloads & links

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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)180,7059
Polymers179,3704
Non-polymers1,3355
Water0
1
A: Uncharacterized ATP-dependent helicase YprA
C: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4495
Polymers89,6852
Non-polymers7643
Water0
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)90,2574
Polymers89,6852
Non-polymers5722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.570, 140.570, 210.066
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 4 or resid 6 through 15...
d_2ens_1(chain "B" and (resid 4 or resid 6 through 15...
d_1ens_2(chain "C" and resid -6 through 6)
d_2ens_2(chain "D" and resid -6 through 6)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLYSA3
d_12ens_1LEUGLYA5 - 14
d_13ens_1GLUPROA16 - 35
d_14ens_1SERSERA37 - 47
d_15ens_1GLYGLNA50 - 66
d_16ens_1GLYGLNA68 - 114
d_17ens_1SERILEA116 - 129
d_18ens_1SERARGA131 - 147
d_19ens_1ALACYSA149 - 208
d_110ens_1PHEVALA210 - 262
d_111ens_1ARGALAA269 - 294
d_112ens_1SERARGA296 - 387
d_113ens_1GLYASPA389 - 447
d_114ens_1GLUGLYA449 - 472
d_115ens_1TYRSERA475 - 479
d_116ens_1SERARGA481 - 490
d_117ens_1ASNASPA496 - 501
d_118ens_1SERVALA503 - 508
d_119ens_1ILEVALA510 - 555
d_120ens_1TYRLEUA557 - 567
d_121ens_1ILETHRA572 - 575
d_122ens_1ASPTRPA587 - 626
d_123ens_1GLUGLUA628
d_124ens_1GLYGLYA647
d_125ens_1SERVALA649 - 658
d_126ens_1ILEHISA660 - 720
d_127ens_1GLYGLYA722 - 728
d_128ens_1GLULEUA738 - 741
d_129ens_1LEUGLNA743 - 746
d_21ens_1LYSLYSB1
d_22ens_1LEUGLYB3 - 12
d_23ens_1GLUPROB14 - 33
d_24ens_1SERSERB35 - 45
d_25ens_1GLYGLNB48 - 64
d_26ens_1GLYGLNB66 - 112
d_27ens_1SERILEB114 - 127
d_28ens_1SERARGB129 - 145
d_29ens_1ALACYSB147 - 206
d_210ens_1PHEVALB208 - 260
d_211ens_1ARGALAB264 - 289
d_212ens_1SERARGB291 - 382
d_213ens_1GLYASPB384 - 442
d_214ens_1GLUGLYB444 - 467
d_215ens_1TYRSERB470 - 474
d_216ens_1SERARGB476 - 485
d_217ens_1ASNASPB491 - 496
d_218ens_1SERVALB498 - 503
d_219ens_1ILEVALB505 - 550
d_220ens_1TYRLEUB552 - 562
d_221ens_1ILETRPB564 - 607
d_222ens_1GLUGLUB609
d_223ens_1GLYGLYB617
d_224ens_1SERVALB619 - 628
d_225ens_1ILEHISB630 - 690
d_226ens_1GLYGLYB692 - 698
d_227ens_1GLULEUB703 - 706
d_228ens_1LEUGLNB708 - 711
d_11ens_2DTDTC
d_21ens_2DTDTD

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.992196169002, 0.0930542450248, 0.0829919857598), (0.0837992009915, 0.990527828578, -0.108776443804), (-0.0923279812987, -0.100972908725, -0.990595788187)123.824564937, 2.31142847144, 175.480326822
2given(-0.995708319865, 0.0528747997646, 0.0759552322181), (0.0408331381905, 0.987513381453, -0.152151162589), (-0.0830517704626, -0.148396687974, -0.985434333896)130.577933824, 10.1295604595, 181.060037586

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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: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.24 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: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.34→50 Å / Num. obs: 31095 / % possible obs: 99.2 % / Redundancy: 14.8 % / Biso Wilson estimate: 64.36 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.45
Reflection shellResolution: 3.34→3.54 Å / Num. unique obs: 4895 / CC1/2: 0.51

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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: 3.34→28.73 Å / SU ML: 0.4983 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2822 1551 5 %
Rwork0.2228 29456 -
obs0.2258 31007 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.68 Å2
Refinement stepCycle: LAST / Resolution: 3.34→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11602 568 77 0 12247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004712546
X-RAY DIFFRACTIONf_angle_d0.854317113
X-RAY DIFFRACTIONf_chiral_restr0.05291932
X-RAY DIFFRACTIONf_plane_restr0.00592104
X-RAY DIFFRACTIONf_dihedral_angle_d19.7281887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.07650614222
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.893053515646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.440.37451370.33472601X-RAY DIFFRACTION98.07
3.44-3.570.35021390.30382646X-RAY DIFFRACTION99.71
3.57-3.710.34611390.25792649X-RAY DIFFRACTION99.93
3.71-3.880.30481390.25412641X-RAY DIFFRACTION99.89
3.88-4.080.30441370.24642595X-RAY DIFFRACTION96.98
4.08-4.340.28681410.21462679X-RAY DIFFRACTION100
4.34-4.670.24461420.18872692X-RAY DIFFRACTION100
4.67-5.140.25221410.19732689X-RAY DIFFRACTION99.93
5.14-5.870.28771430.22222719X-RAY DIFFRACTION99.65
5.88-7.380.29191430.22372708X-RAY DIFFRACTION98.55
7.38-28.730.24341500.18712837X-RAY DIFFRACTION97.65

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