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- PDB-6jtz: Crystal Structure of hRecQ1_D2-Zn-WH containing mutation on beta-... -

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Basic information

Entry
Database: PDB / ID: 6jtz
TitleCrystal Structure of hRecQ1_D2-Zn-WH containing mutation on beta-hairpin
ComponentsATP-dependent DNA helicase Q1
KeywordsDNA BINDING PROTEIN / RecQ1 / Helicase / DNA-binding protein / Zn-binding domain
Function / homology
Function and homology information


double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / mediator complex / DNA 3'-5' helicase / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity ...double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / mediator complex / DNA 3'-5' helicase / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity / double-strand break repair via homologous recombination / chromosome / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
RQC domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...RQC domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding 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 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.797 Å
AuthorsDas, T. / Mukhopadhyay, S. / Bose, M. / Das, A.K. / Ganguly, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India) India
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Residues at the interface between zinc binding and winged helix domains of human RECQ1 play a significant role in DNA strand annealing activity.
Authors: Mukhopadhyay, S. / Das, T. / Bose, M. / Jain, C.K. / Chakraborty, M. / Mukherjee, S. / Shikha, K. / Das, A.K. / Ganguly, A.
History
DepositionApr 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q1
B: ATP-dependent DNA helicase Q1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3824
Polymers80,2512
Non-polymers1312
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer in ASU
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-15 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.950, 101.835, 73.434
Angle α, β, γ (deg.)90.000, 99.070, 90.000
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: 40125.648 Da / Num. of mol.: 2 / Fragment: UNP residues 285-592 / Mutation: del(561,562,565,566), Y564A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL, RECQ1, RECQL1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3) / References: UniProt: P46063, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 65% v/v Tacsimate pH=7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.797→72.516 Å / Num. obs: 18892 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 38.97 Å2 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1 / Rsym value: 0.086 / Net I/av σ(I): 8.3 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.8-2.953.80.3662.127090.2170.4260.36698
2.95-3.133.80.258326080.1530.3010.25899.1
3.13-3.343.80.1574.924380.0930.1830.15799.2
3.34-3.613.80.1047.222890.0620.1210.10499.6
3.61-3.963.80.0789.420970.0470.0910.07899.6
3.96-4.423.80.05611.919390.0330.0650.05699.8
4.42-5.113.80.0512.816810.030.0580.0599.7
5.11-6.263.80.05811.614370.0350.0680.05899.9
6.26-8.853.70.0431511270.0260.050.04399.7
8.85-19.693.60.03119.75670.0190.0360.03190.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V1X

2v1x


Resolution: 2.797→19.69 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.2817 950 5.03 %
Rwork0.2265 --
obs0.2293 18879 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.9 Å2 / Biso mean: 39.0775 Å2 / Biso min: 10.94 Å2
Refinement stepCycle: final / Resolution: 2.797→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4787 0 2 139 4928
Biso mean--47.76 33.09 -
Num. residues----604
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7974-2.94440.3731380.27482511264998
2.9444-3.12820.36141400.27352534267499
3.1282-3.36870.35791180.2462570268899
3.3687-3.70560.28241380.222425522690100
3.7056-4.23720.28911430.215625632706100
4.2372-5.32090.22241360.194425792715100
5.3209-19.69050.23781370.224526202757100

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