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

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Basic information

Entry
Database: PDB / ID: 5gju
TitleDEAD-box RNA helicase
ComponentsATP-dependent RNA helicase DeaD
KeywordsHYDROLASE / RecA-like / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ATP-dependent RNA helicase DeaD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXu, L. / Li, F. / Wang, 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
DepositionJul 2, 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 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9082
Polymers22,5611
Non-polymers3471
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-4 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 57.990, 104.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 22561.170 Da / Num. of mol.: 1 / Fragment: UNP residues 6-210
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 (E. coli) / References: UniProt: P0A9P6, RNA helicase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.1M DL-Malic acid, pH 7.0, 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: Nov 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50.221 Å / Num. all: 26166 / Num. obs: 26166 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.83 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Rsym value: 0.084 / Net I/av σ(I): 6.915 / Net I/σ(I): 12.5 / Num. measured all: 161038
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.696.20.5911.32356138070.2550.6450.5913.4100
1.69-1.796.20.4071.82236236070.1760.4440.4074.7100
1.79-1.916.20.24932101133910.1080.2720.2496.8100
1.91-2.076.20.1514.91970731880.0660.1650.15110100
2.07-2.266.20.1086.71791328990.0470.1180.10813.5100
2.26-2.536.10.09771627626470.0430.1070.09716.1100
2.53-2.925.90.097.21385723290.040.0990.0919.2100
2.92-3.585.80.06110.41137919540.0270.0660.0612499.5
3.58-5.066.50.03916.4996015280.0160.0420.03930.599.6
5.06-28.9956.10.0411550128160.0180.0450.04128.296.1

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gxs

2gxs


Resolution: 1.6→28.995 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 1331 5.09 %
Rwork0.1668 24806 -
obs0.1687 26137 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.28 Å2 / Biso mean: 23.6998 Å2 / Biso min: 6.79 Å2
Refinement stepCycle: final / Resolution: 1.6→28.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 35 208 1774
Biso mean--21.47 32.34 -
Num. residues----199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011579
X-RAY DIFFRACTIONf_angle_d1.1582141
X-RAY DIFFRACTIONf_chiral_restr0.056254
X-RAY DIFFRACTIONf_plane_restr0.008275
X-RAY DIFFRACTIONf_dihedral_angle_d12.101978
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 (%)
1.6-1.65720.26251180.23124962614100
1.6572-1.72350.25871300.206524632593100
1.7235-1.8020.24761350.20424832618100
1.802-1.8970.23411390.187324762615100
1.897-2.01580.23511260.171724792605100
2.0158-2.17140.20041330.161824852618100
2.1714-2.38980.18771510.153824682619100
2.3898-2.73540.18921300.157124942624100
2.7354-3.44540.20641400.163424732613100
3.4454-28.99970.18211290.15552489261899

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