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- PDB-5b88: RRM-like domain of DEAD-box protein, CsdA -

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Basic information

Entry
Database: PDB / ID: 5b88
TitleRRM-like domain of DEAD-box protein, CsdA
ComponentsATP-dependent RNA helicase DeaD
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


RNA strand annealing activity / mRNA stabilization / RNA catabolic process / cellular response to cold / response to cold / positive regulation of translation / response to radiation / ribosomal large subunit assembly / RNA helicase activity / RNA helicase ...RNA strand annealing activity / mRNA stabilization / RNA catabolic process / cellular response to cold / response to cold / positive regulation of translation / response to radiation / ribosomal large subunit assembly / RNA helicase activity / RNA helicase / protein homodimerization activity / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Cold-shock protein, DEAD box A, C-terminal / ATP-dependent RNA helicase DeaD / CsdA, RNA recognition motif / DeaD helicase C-terminal disordered region / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif ...Cold-shock protein, DEAD box A, C-terminal / ATP-dependent RNA helicase DeaD / CsdA, RNA recognition motif / DeaD helicase C-terminal disordered region / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase DeaD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsXu, L. / Peng, J. / Zhang, J. / Wu, J. / Tang, Y. / Shi, Y.
CitationJournal: Structure / Year: 2017
Title: Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.
Authors: Xu, L. / Wang, L. / Peng, J. / Li, F. / Wu, L. / Zhang, B. / Lv, M. / Zhang, J. / Gong, Q. / Zhang, R. / Zuo, X. / Zhang, Z. / Wu, J. / Tang, Y. / Shi, Y.
History
DepositionJun 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 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: ATP-dependent RNA helicase DeaD


Theoretical massNumber of molelcules
Total (without water)9,4491
Polymers9,4491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6100 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein ATP-dependent RNA helicase DeaD / Cold-shock DEAD box protein A / Translation factor W2


Mass: 9448.825 Da / Num. of mol.: 1 / Fragment: RRM-like domain, UNP residues 482-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: deaD / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9P6, RNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D CBCA(CO)NH
142isotropic13D C(CO)NH
152isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
172isotropic13D HN(CA)CB
182isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] RRM-like domain, 100% D2O15N,13C_SD2O100% D2O
solution21 mM [U-99% 13C; U-99% 15N] RRM-like domain, 90% H2O/10% D2O15N,13C_SH2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRRM-like domain[U-99% 13C; U-99% 15N]1
1 mMRRM-like domain[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 25 C

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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