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- PDB-5gi4: DEAD-box RNA helicase -

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Basic information

Entry
Database: PDB / ID: 5gi4
TitleDEAD-box RNA helicase
ComponentsATP-dependent RNA helicase DeaD
KeywordsHYDROLASE / Dimer / RecA-like / Wild type / RNA helicase
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsXu, L. / Wang, L. / Li, F. / Wu, L. / 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 22, 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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DeaD
B: ATP-dependent RNA helicase DeaD


Theoretical massNumber of molelcules
Total (without water)51,4992
Polymers51,4992
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-37 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.617, 86.985, 117.851
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25749.334 Da / Num. of mol.: 2 / Fragment: UNP residues 218-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: deaD, csdA, mssB, rhlD, b3162, JW5531 / Production host: Escherichia coli (strain K12) (bacteria) / Strain (production host): K12 / References: UniProt: P0A9P6, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 2000, 2mM magnesium chloride, 0.1M Tris, 0.2M Trimethylamine N-oxide dihydrate, 2mM AMP-PNP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.244→50 Å / Num. obs: 27715 / % possible obs: 98.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 43.49 Å2 / Rmerge(I) obs: 0.074 / Net I/av σ(I): 27.882 / Net I/σ(I): 11
Reflection shellResolution: 2.244→2.33 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.607 / CC1/2: 0.855 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.244→34.993 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.11
RfactorNum. reflection% reflection
Rfree0.2683 1344 4.86 %
Rwork0.225 --
obs0.2271 27662 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.81 Å2 / Biso mean: 58.4733 Å2 / Biso min: 28.63 Å2
Refinement stepCycle: final / Resolution: 2.244→34.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 0 183 3714
Biso mean---54.05 -
Num. residues----445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093571
X-RAY DIFFRACTIONf_angle_d1.1024816
X-RAY DIFFRACTIONf_chiral_restr0.054554
X-RAY DIFFRACTIONf_plane_restr0.005633
X-RAY DIFFRACTIONf_dihedral_angle_d18.1242228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2439-2.32410.40121140.34642416253092
2.3241-2.41710.37611280.30712607273598
2.4171-2.52710.30981170.281826382755100
2.5271-2.66030.35691280.268726282756100
2.6603-2.82690.33761360.269126232759100
2.8269-3.0450.30821470.267726322779100
3.045-3.35120.27911290.249126812810100
3.3512-3.83560.2741560.220726472803100
3.8356-4.83050.24111420.18462680282299
4.8305-34.99720.20591470.18572766291397

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