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- PDB-6crm: Crystal Structure of RecQ catalytic core from C. sakazakii bound ... -

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Basic information

Entry
Database: PDB / ID: 6crm
TitleCrystal Structure of RecQ catalytic core from C. sakazakii bound to an unfolded G-quadruplex
Components
  • DNA (5'-D(P*GP*GP*GP*TP*CP*GP*GP*TP*GP*CP*CP*TP*TP*A)-3')
  • RecQ
KeywordsHYDROLASE/DNA / G-quadruplex / Helicase / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


3'-5' DNA helicase activity / SOS response / DNA recombination / DNA replication / DNA helicase / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA helicase, ATP-dependent, RecQ type, bacterial / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain ...DNA helicase, ATP-dependent, RecQ type, bacterial / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / HRDC-like superfamily / 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 nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA helicase
Similarity search - Component
Biological speciesCronobacter sakazakii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19286241172 Å
AuthorsVoter, A.F. / Keck, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098885 United States
CitationJournal: Nat Commun / Year: 2018
Title: A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases.
Authors: Voter, A.F. / Qiu, Y. / Tippana, R. / Myong, S. / Keck, J.L.
History
DepositionMar 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: RecQ
B: DNA (5'-D(P*GP*GP*GP*TP*CP*GP*GP*TP*GP*CP*CP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0813
Polymers72,0162
Non-polymers651
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-20 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.468, 94.670, 98.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-800-

HOH

21A-824-

HOH

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Components

#1: Protein RecQ


Mass: 60445.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Exact C-terminus not defined, the HRDC domain was removed with thrombin
Source: (gene. exp.) Cronobacter sakazakii (strain ATCC BAA-894) (bacteria)
Strain: ATCC BAA-894 / Gene: ESA_03738 / Production host: Escherichia coli (E. coli) / References: UniProt: A7MQK9
#2: DNA chain DNA (5'-D(P*GP*GP*GP*TP*CP*GP*GP*TP*GP*CP*CP*TP*TP*A)-3')


Mass: 11570.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 / Details: 70 mM NaOAc, 10% PEG 4000, 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.127231 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127231 Å / Relative weight: 1
ReflectionResolution: 2.192→43.833 Å / Num. obs: 38101 / % possible obs: 99.1 % / Redundancy: 13 % / Biso Wilson estimate: 53.3012096157 Å2 / Rmerge(I) obs: 0.1507 / Rpim(I) all: 0.04362 / Rrim(I) all: 0.1571 / Net I/σ(I): 11.35
Reflection shellResolution: 2.194→2.272 Å / Redundancy: 11.3 % / Rmerge(I) obs: 2.887 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 3473 / Rpim(I) all: 0.8546 / Rrim(I) all: 3.018 / % possible all: 92.63

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata scaling
PHENIXphasing
PHENIXmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMU

4tmu


Resolution: 2.19286241172→43.832890357 Å / SU ML: 0.42920099339 / Cross valid method: THROUGHOUT / σ(F): 1.32758362296 / Phase error: 33.8956660332
RfactorNum. reflection% reflection
Rfree0.239823580985 1992 5.23287887146 %
Rwork0.205005626627 --
obs0.206815513409 38067 98.9910284748 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.19286241172→43.832890357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 290 1 142 4450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00370516094914436
X-RAY DIFFRACTIONf_angle_d0.6667828560716067
X-RAY DIFFRACTIONf_chiral_restr0.0443443602806671
X-RAY DIFFRACTIONf_plane_restr0.00466282409479753
X-RAY DIFFRACTIONf_dihedral_angle_d22.67805235511692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1929-2.24770.5681820632311240.5215997478772260X-RAY DIFFRACTION88.1005173688
2.2477-2.30850.4517322997911480.4036764321072539X-RAY DIFFRACTION99.8513563731
2.3085-2.37640.3925304493951280.3659421844612568X-RAY DIFFRACTION99.7410284869
2.3764-2.45310.3767066266021540.3301881958082553X-RAY DIFFRACTION99.7420781135
2.4531-2.54080.3449323308391320.3021031206682585X-RAY DIFFRACTION99.8897058824
2.5408-2.64250.3409762955881490.2984122168972541X-RAY DIFFRACTION99.8886000743
2.6425-2.76270.3579682439691430.2817623810732566X-RAY DIFFRACTION99.7790055249
2.7627-2.90830.2872812224531410.2221967045262615X-RAY DIFFRACTION99.9274836838
2.9083-3.09050.2818884661871460.2088472739152585X-RAY DIFFRACTION99.8902706657
3.0905-3.32910.2329490043411410.1943538425842593X-RAY DIFFRACTION99.9634369287
3.3291-3.66390.2181338313531430.1798474944012615X-RAY DIFFRACTION99.9275362319
3.6639-4.19370.2120042288341460.1611548817252624X-RAY DIFFRACTION100
4.1937-5.28220.1691966398881430.1515608892272670X-RAY DIFFRACTION99.7517730496
5.2822-43.84160.1924645451971540.1851902786232761X-RAY DIFFRACTION99.2847411444
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9323240264-0.6625111523130.7753893265951.87069317258-0.09313653872661.865770730020.0223719062552-0.234458535117-0.04066064222020.0628797888461-0.0049070780220.04903365547770.0326312158876-0.0384737987928-0.01287097978610.416168856321-0.02056468328920.0164607188460.401284191767-0.008756492860080.83558658290114.149007592811.372070292457.9596178832
22.98226881470.174482667341-0.5634384745911.91318164961-0.2979954352742.285261934070.03129831294550.214747037368-0.0621191171392-0.241278643604-0.0371612041565-0.2894775205460.0815823858450.1942390219170.0001958073825030.3427275673260.008318534020460.03810261961260.396211680463-0.02713556652920.7829705644178.5811734713524.07769443233.9675292565
33.660037169871.003523095522.460660809013.966981464031.687029110158.16343765488-0.09664205660371.357029159680.286751165381-0.8884190066030.006590128841880.07830235710760.126640550881-0.04135569435110.06830315032430.6182220978530.02807605667950.03328919804051.093690439020.03744853671950.796340043685-10.882991862929.264635883711.3584541695
45.226393738422.38475053566-1.697657165176.768129169381.99860898682.00198669390.2825660829390.3947361437930.00801764306118-0.8012056806650.3323653638290.3706199689830.792196063807-0.536254140812-0.3062971128950.5827298175620.08631934574040.04683201606840.501304237126-0.1371485030130.83844961109312.14861748636.9434431304829.80202829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 196 )
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 400 )
3X-RAY DIFFRACTION3chain 'A' and (resid 401 through 516 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 32 )

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