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- PDB-8yrs: Crystal structure of human RECQ1 helicase containing a flexible l... -

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Basic information

Entry
Database: PDB / ID: 8yrs
TitleCrystal structure of human RECQ1 helicase containing a flexible linker in complex with tailed duplex DNA
Components
  • ATP-dependent DNA helicase Q1
  • DNA (27-MER)
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*C)-3')
KeywordsDNA BINDING PROTEIN / Helicase / zinc-binding domain / winged-helix / tailed-duplex DNA
Function / homology
Function and homology information


DNA/DNA annealing activity / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / DNA helicase activity / isomerase activity / double-strand break repair via homologous recombination / chromosome / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity ...DNA/DNA annealing activity / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / DNA helicase activity / isomerase activity / double-strand break repair via homologous recombination / chromosome / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / 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 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 ...ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent DNA helicase Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsDas, T. / Das, A.K. / Ganguly, A.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2022/005602 India
CitationJournal: To Be Published
Title: Crystal structure of human RECQ1 helicase containing a flexible linker in complex with tailed duplex DNA
Authors: Das, T. / Das, A.K. / Ganguly, A.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q1
B: ATP-dependent DNA helicase Q1
C: DNA (5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*C)-3')
D: DNA (27-MER)
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*C)-3')
Q: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3218
Polymers159,1906
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.323, 96.573, 96.806
Angle α, β, γ (deg.)90.00, 106.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent DNA helicase Q1 / DNA helicase / RecQ-like type 1 / RecQ1 / DNA-dependent ATPase Q1 / RecQ protein-like 1


Mass: 67408.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: human RECQ1 helicase containing a flexible linker (GGGGSGGGGS) inserted between residues 480 (K) and 491 (D)
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL, RECQ1, RECQL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46063, DNA helicase
#2: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*C)-3')


Mass: 3976.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 13-mer DNA / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (27-MER)


Mass: 8210.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 27-mer DNA / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: 2.45 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Sodium malonate (pH=7.0) and 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Dec 22, 2023
Details: Both CM and TM are 1.2 m single-crystal Si with Rh coating
RadiationMonochromator: Water-cooled DCM with Si (111) or Si (220) crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.43→48.28 Å / Num. obs: 35793 / % possible obs: 92.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 40.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.064 / Rrim(I) all: 0.124 / Net I/σ(I): 9.6
Reflection shellResolution: 2.43→2.57 Å / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 359 / CC1/2: 0.536 / Rpim(I) all: 0.628 / Rrim(I) all: 1.22 / % possible all: 53.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
STARANISOdata scaling
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WWY

2wwy


Resolution: 2.43→46.64 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1999 5.59 %
Rwork0.2375 --
obs0.2386 35777 64.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8436 1397 2 0 9835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.414
X-RAY DIFFRACTIONf_dihedral_angle_d24.8071814
X-RAY DIFFRACTIONf_chiral_restr0.0781563
X-RAY DIFFRACTIONf_plane_restr0.0141542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.490.413150.392394X-RAY DIFFRACTION3
2.5-2.560.3684130.4062200X-RAY DIFFRACTION5
2.56-2.640.2457260.3419459X-RAY DIFFRACTION12
2.64-2.720.3808410.3766675X-RAY DIFFRACTION18
2.72-2.820.431680.35741163X-RAY DIFFRACTION31
2.82-2.930.3641130.35151895X-RAY DIFFRACTION51
2.93-3.070.36391900.33333219X-RAY DIFFRACTION87
3.07-3.230.30642210.31083735X-RAY DIFFRACTION100
3.23-3.430.29752180.27943691X-RAY DIFFRACTION100
3.43-3.70.2882190.25153693X-RAY DIFFRACTION100
3.7-4.070.23412190.22433706X-RAY DIFFRACTION100
4.07-4.660.22162220.19343730X-RAY DIFFRACTION100
4.66-5.860.23292200.20133734X-RAY DIFFRACTION100
5.86-46.640.19972240.1923784X-RAY DIFFRACTION99
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)
12.6345-0.38950.24693.5636-1.61816.9227-0.09220.4145-0.07810.06910.005-0.12950.22011.01040.01890.2299-0.03550.00620.436-0.06640.328438.820214.937841.8977
23.7041-0.29270.56961.4518-0.08632.7972-0.17130.13270.3380.00180.0582-0.0048-0.4190.15590.05850.355-0.0684-0.06870.13220.04170.158714.403518.301912.9981
30.40680.30070.38870.22530.35310.71010.0749-0.13410.2933-0.2072-1.08921.4245-0.7284-2.37250.33510.92210.72840.0731.961-0.74030.8331-13.959826.078154.1124
40.6535-0.7286-0.24592.22373.07456.28760.1311-0.38150.0684-0.2985-0.57430.1227-0.1593-1.75910.24270.42080.0221-0.01450.8826-0.08980.3441-4.550814.507143.9889
53.70550.98530.5141.3310.36852.1734-0.0126-0.0814-0.11040.073-0.05830.04910.0877-0.34230.06210.26830.02310.00090.1917-0.04640.124617.770316.890775.3382
61.55440.0664-0.49580.73870.68643.75670.7611-0.6318-0.40471.1790.2165-0.65770.30870.5941-0.8480.9859-0.0835-0.38380.368-0.05630.39543.19392.601287.8594
72.00024.95898.25662.96362.92948.33450.65773.2854-3.7283-0.63781.27110.03531.13771.1197-1.82920.4446-0.0803-0.16911.1488-0.22311.104663.01916.8108115.6953
83.0299-0.7479-0.23043.0179-0.19120.03940.2803-0.37810.46460.3192-0.275-0.1980.98520.876-0.05950.83810.1652-0.08610.7899-0.06290.76345.48192.96596.8382
91.6617-1.181-0.58981.96370.1550.9812-0.2582-0.069-0.47480.4709-0.14470.4620.6052-0.1376-0.33480.6040.10120.20.1439-0.13940.264126.29220.744468.5865
101.84040.2856-2.23570.0431-0.34662.71620.2566-0.44460.4237-0.00881.1574-0.4503-0.5820.5537-1.28222.79570.2664-0.62541.2384-0.22522.0059-11.58923.3029-1.0568
114.84933.31733.69662.27782.53262.8206-0.40510.3449-2.63990.47670.60630.44650.31980.1802-0.26912.35230.073-0.08592.0871-0.14021.8384-14.23131.2225-7.9949
120.383-0.11960.14780.1426-0.14060.14230.6341-0.9625-0.2168-0.71420.15570.5611.5673-0.5627-0.74052.1228-0.06370.34853.0251-0.48812.2366-4.80571.772916.3842
134.29370.2513-3.67757.78090.65415.1464-0.2107-0.77620.08670.20950.26960.062-0.0613-0.486-0.00171.1164-0.0481-0.21780.84770.37110.770312.71097.536626.5628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 62 through 285 )
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 602 )
3X-RAY DIFFRACTION3chain 'B' and (resid 63 through 118 )
4X-RAY DIFFRACTION4chain 'B' and (resid 119 through 285 )
5X-RAY DIFFRACTION5chain 'B' and (resid 286 through 602 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'D' and (resid 2 through 6 )
8X-RAY DIFFRACTION8chain 'D' and (resid 7 through 16 )
9X-RAY DIFFRACTION9chain 'D' and (resid 17 through 25 )
10X-RAY DIFFRACTION10chain 'P' and (resid 1 through 13 )
11X-RAY DIFFRACTION11chain 'Q' and (resid 7 through 16 )
12X-RAY DIFFRACTION12chain 'Q' and (resid 17 through 21 )
13X-RAY DIFFRACTION13chain 'Q' and (resid 22 through 25 )

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