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- PDB-1s2m: Crystal Structure of the DEAD box protein Dhh1p -

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Basic information

Entry
Database: PDB / ID: 1s2m
TitleCrystal Structure of the DEAD box protein Dhh1p
ComponentsPutative ATP-dependent RNA helicase DHH1
KeywordsRNA BINDING PROTEIN / ATP-binding / RNA-binding / Helicase
Function / homology
Function and homology information


regulation of cytoplasmic mRNA processing body assembly / mRNA decay by 5' to 3' exoribonuclease / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / mRNA transport / stress granule assembly / positive regulation of translation / P-body ...regulation of cytoplasmic mRNA processing body assembly / mRNA decay by 5' to 3' exoribonuclease / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / mRNA transport / stress granule assembly / positive regulation of translation / P-body / mRNA processing / cytoplasmic stress granule / negative regulation of translation / RNA helicase activity / RNA helicase / mRNA binding / chromatin binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
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 / DEAD/DEAH box helicase domain / 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-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 / DEAD/DEAH box helicase domain / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DHH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCheng, Z. / Song, H.
CitationJournal: Rna / Year: 2005
Title: Crystal structure and functional analysis of DEAD-box protein Dhh1p.
Authors: Cheng, Z. / Coller, J. / Parker, R. / Song, H.
History
DepositionJan 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ATP-dependent RNA helicase DHH1


Theoretical massNumber of molelcules
Total (without water)45,2681
Polymers45,2681
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.210, 80.410, 54.824
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative ATP-dependent RNA helicase DHH1 / Dead box RNA Helicase Dhh1p


Mass: 45268.289 Da / Num. of mol.: 1 / Fragment: core RNA Helicase fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DHH1, YDL160C / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Ril / References: UniProt: P39517
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.29 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MES, Potassium bromide, PEG400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9195, 0.9198, 0.9134
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2003
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91951
20.91981
30.91341
ReflectionResolution: 2.1→30 Å / Num. all: 24039 / Num. obs: 23923 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.12→2.22 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.067 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.249 / ESU R Free: 0.189
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23356 1204 5 %RANDOM
Rwork0.20049 ---
obs0.20216 22719 99.52 %-
all-24039 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.97 Å2
2---0.08 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 253 3261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223063
X-RAY DIFFRACTIONr_bond_other_d0.0020.022879
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9644137
X-RAY DIFFRACTIONr_angle_other_deg0.76336696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765376
X-RAY DIFFRACTIONr_chiral_restr0.0660.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02612
X-RAY DIFFRACTIONr_nbd_refined0.1920.2642
X-RAY DIFFRACTIONr_nbd_other0.2280.23319
X-RAY DIFFRACTIONr_nbtor_other0.0780.21783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.212
X-RAY DIFFRACTIONr_mcbond_it0.6151.51878
X-RAY DIFFRACTIONr_mcangle_it1.18423050
X-RAY DIFFRACTIONr_scbond_it1.58131185
X-RAY DIFFRACTIONr_scangle_it2.784.51087
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 85
Rwork0.203 1628

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