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- PDB-2ma1: Solution structure of HRDC1 domain of RecQ helicase from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 2ma1
TitleSolution structure of HRDC1 domain of RecQ helicase from Deinococcus radiodurans
ComponentsDNA helicase RecQ
KeywordsDNA BINDING PROTEIN / RecQ HRDC domain 1
Function / homology
Function and homology information


bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / DNA 3'-5' helicase / DNA duplex unwinding / 3'-5' DNA helicase activity / isomerase activity / chromosome / DNA recombination ...bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / DNA 3'-5' helicase / DNA duplex unwinding / 3'-5' DNA helicase activity / isomerase activity / chromosome / DNA recombination / DNA replication / hydrolase activity / DNA repair / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA helicase, ATP-dependent, RecQ type, bacterial / HRDC domain / 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 ...DNA helicase, ATP-dependent, RecQ type, bacterial / HRDC domain / 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 domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLiu, S. / Zhang, W. / Gao, Z. / Ming, Q. / Hou, H. / Lan, W. / Wu, H. / Cao, C. / Dong, Y.
CitationJournal: To be Published
Title: NMR structure of the N-terminal-most HRDC1 domain of RecQ helicase from Deinococcus radiodurans
Authors: Liu, S. / Zhang, W. / Gao, Z. / Ming, Q. / Hou, H. / Lan, W. / Wu, H. / Cao, C. / Dong, Y.
History
DepositionJun 24, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA helicase RecQ


Theoretical massNumber of molelcules
Total (without water)8,0541
Polymers8,0541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA helicase RecQ


Mass: 8054.140 Da / Num. of mol.: 1 / Fragment: UNP residues 536-610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DrRecQ, DR_1289 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RUU2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1313D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 2mM [U-98% 13C; U-98% 15N] HRDC1-1, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: HRDC1-1 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 0.05 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1230 / NOE intraresidue total count: 397 / NOE long range total count: 103 / NOE medium range total count: 338 / NOE sequential total count: 392 / Hydrogen bond constraints total count: 26 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 48 / Protein psi angle constraints total count: 48
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures for lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 1 / Representative conformer: 1

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