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- PDB-7a8r: Structure of RecQL from Bos taurus -

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Basic information

Entry
Database: PDB / ID: 7a8r
TitleStructure of RecQL from Bos taurus
ComponentsATP-dependent DNA helicase
KeywordsRECOMBINATION / helicase / DNA repair / Holliday junction
Function / homology
Function and homology information


four-way junction helicase activity / ATP-dependent DNA/DNA annealing activity / DNA duplex unwinding / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / double-strand break repair via homologous recombination / chromosome / DNA recombination / DNA helicase / DNA repair ...four-way junction helicase activity / ATP-dependent DNA/DNA annealing activity / DNA duplex unwinding / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / double-strand break repair via homologous recombination / chromosome / DNA recombination / DNA helicase / DNA repair / nucleoplasm / ATP binding / cytoplasm
Similarity search - Function
ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 ...ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent DNA helicase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsRety, S. / Chen, W.F. / Xi, X.G.
CitationJournal: Cell Rep / Year: 2021
Title: Endogenous Bos taurus RECQL is predominantly monomeric and more active than oligomers.
Authors: Liu, N.N. / Song, Z.Y. / Guo, H.L. / Yin, H. / Chen, W.F. / Dai, Y.X. / Xin, B.G. / Ai, X. / Ji, L. / Wang, Q.M. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G.
History
DepositionAug 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase
B: ATP-dependent DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1448
Polymers121,1112
Non-polymers1,0346
Water1,69394
1
A: ATP-dependent DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0724
Polymers60,5551
Non-polymers5173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0724
Polymers60,5551
Non-polymers5173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.576, 117.224, 203.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ATP-dependent DNA helicase


Mass: 60555.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RECQL
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0JN36, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 20K 11-16% Hepes 100mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.31→23.16 Å / Num. obs: 44709 / % possible obs: 91.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 49.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 2.32→2.539 Å / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2235 / CC1/2: 0.443 / Rpim(I) all: 0.545 / Rrim(I) all: 0.866

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSBUILT 20190315)data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U7D

4u7d


Resolution: 2.31→23.16 Å / SU ML: 0.2637 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.6981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 2299 5.15 %
Rwork0.2014 42380 -
obs0.204 44679 75.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.89 Å2
Refinement stepCycle: LAST / Resolution: 2.31→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8466 0 58 94 8618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00428700
X-RAY DIFFRACTIONf_angle_d0.809611740
X-RAY DIFFRACTIONf_chiral_restr0.04711295
X-RAY DIFFRACTIONf_plane_restr0.00441479
X-RAY DIFFRACTIONf_dihedral_angle_d20.79673298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.3537100.2856216X-RAY DIFFRACTION6.25
2.36-2.410.2469150.3055330X-RAY DIFFRACTION9.35
2.41-2.470.2812240.2883570X-RAY DIFFRACTION16.58
2.47-2.540.2863590.29271104X-RAY DIFFRACTION31.31
2.54-2.620.31691120.29122021X-RAY DIFFRACTION58.41
2.62-2.70.31291520.29092853X-RAY DIFFRACTION81.97
2.7-2.80.32931660.28233335X-RAY DIFFRACTION94.39
2.8-2.910.35431830.27393485X-RAY DIFFRACTION99.95
2.91-3.040.29721940.26173461X-RAY DIFFRACTION99.89
3.04-3.20.28112250.263474X-RAY DIFFRACTION100
3.2-3.40.29711830.22893543X-RAY DIFFRACTION100
3.4-3.660.28581810.20233555X-RAY DIFFRACTION99.95
3.66-4.030.25742050.1843517X-RAY DIFFRACTION99.84
4.03-4.610.21561790.15273585X-RAY DIFFRACTION99.95
4.61-5.790.21932040.1653577X-RAY DIFFRACTION99.71
5.79-23.160.1842070.16983754X-RAY DIFFRACTION99.5
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)
11.80692481411-0.0544847376306-0.3537656469023.470323989261.427509397795.227280387760.0813275122972-0.09674229399050.1005790241730.276671418627-0.09398700740880.0495532949378-0.4986018790620.003407485459210.0008369232661370.55873308233-0.0260355783494-0.02384119662070.3126418700150.03114786717890.27882822106623.447401513438.558078361390.8215445329
20.7996433964020.1222147147510.1364281627361.91447632951-0.2870537322863.092685815260.0463180160998-0.1275394207680.1087952348240.2392721110240.01069716004280.2191686012360.059263908449-0.395751417345-0.08426581543380.210265971877-0.04906199387330.07437682389740.354094456645-0.05602339394570.3735155043488.3051806098631.296444989258.4515054712
32.86813271959-2.304589683590.519360109662.62148482519-0.6864750810930.8774167511870.04955303990440.05769243578680.313096651847-0.189622110851-0.0800471500293-0.4707124671620.1154041906730.07845424043990.03223336628770.271013308092-0.06264807353110.09737052857850.387220402833-0.03316799601410.52413124357942.201414937911.223101426741.6417383363
41.53313904834-0.4971827274790.3477561646082.984327921850.4194228325722.850931534120.2994357846480.251344158316-0.000515280804308-0.97783878604-0.270164911448-0.1372338774250.299141053073-0.033788927029-0.02995628464240.7785476358310.08004537297650.1257450632540.3821698632090.0447213050550.37325583460521.151220111517.16697076512.4185575266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 62 through 285 )AA62 - 2851 - 224
22chain 'A' and (resid 286 through 592 )AA286 - 592225 - 531
33chain 'B' and (resid 63 through 285 )BE63 - 2851 - 223
44chain 'B' and (resid 286 through 592 )BE286 - 592224 - 530

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