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- PDB-8pnk: Crystal structure of the Ded1p RecA1 domain -

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Basic information

Entry
Database: PDB / ID: 8pnk
TitleCrystal structure of the Ded1p RecA1 domain
ComponentsATP-dependent RNA helicase DED1
KeywordsRNA BINDING PROTEIN / Ded1p / helicase / RecA
Function / homology
Function and homology information


positive regulation of formation of translation preinitiation complex / spliceosomal complex disassembly / eukaryotic initiation factor 4G binding / RNA strand annealing activity / Neutrophil degranulation / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA helicase activity / RNA helicase ...positive regulation of formation of translation preinitiation complex / spliceosomal complex disassembly / eukaryotic initiation factor 4G binding / RNA strand annealing activity / Neutrophil degranulation / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / 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. ...Ded1/Dbp1, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase DED1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuebner, J. / Sprangers, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)418960343 Germany
CitationJournal: To Be Published
Title: Crystal structure of the Ded1p RecA1 domain
Authors: Huebner, J. / Sprangers, R.
History
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DED1


Theoretical massNumber of molelcules
Total (without water)31,7981
Polymers31,7981
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.000, 110.000, 52.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein ATP-dependent RNA helicase DED1 / DEAD box protein 1 / Defines essential domain protein 1


Mass: 31798.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DED1, SPP81, YOR204W / Production host: Escherichia coli (E. coli) / References: UniProt: P06634, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000036 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000036 Å / Relative weight: 1
ReflectionResolution: 2.2→47.63 Å / Num. obs: 18435 / % possible obs: 99.66 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.87 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04857 / Rpim(I) all: 0.02025 / Rrim(I) all: 0.0527 / Net I/σ(I): 21.69
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.7115 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 1764 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.3181 / Rrim(I) all: 0.7811 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.63 Å / SU ML: 0.2058 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.5117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 922 5 %
Rwork0.1891 17509 -
obs0.1908 18431 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 0 45 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252025
X-RAY DIFFRACTIONf_angle_d0.54072745
X-RAY DIFFRACTIONf_chiral_restr0.0433306
X-RAY DIFFRACTIONf_plane_restr0.0049360
X-RAY DIFFRACTIONf_dihedral_angle_d4.514274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.25281270.22922423X-RAY DIFFRACTION98.11
2.32-2.460.28021310.2112492X-RAY DIFFRACTION99.96
2.46-2.650.24011320.20692513X-RAY DIFFRACTION100
2.65-2.920.25231310.21292492X-RAY DIFFRACTION100
2.92-3.340.30811320.21772504X-RAY DIFFRACTION99.96
3.34-4.210.22091330.18682514X-RAY DIFFRACTION99.96
4.21-47.630.1831360.16612571X-RAY DIFFRACTION99.74

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