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- PDB-3moj: Structure of the RNA binding domain of the Bacillus subtilis YxiN... -

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Basic information

Entry
Database: PDB / ID: 3moj
TitleStructure of the RNA binding domain of the Bacillus subtilis YxiN protein complexed with a fragment of 23S ribosomal RNA
Components
  • ATP-dependent RNA helicase dbpA
  • RNA (69-MER)
KeywordsRNA binding protein/RNA / RNA / RNA recognition motif / RNA binding protein / ribosomal RNA / RNA binding protein-RNA complex
Function / homology
Function and homology information


RNA strand annealing activity / 3'-5' RNA helicase activity / response to cold / ribosomal large subunit assembly / RNA helicase activity / RNA helicase / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
ATP-dependent RNA helicase DbpA / 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. / RRM (RNA recognition motif) domain / DEAD/DEAH box helicase domain ...ATP-dependent RNA helicase DbpA / 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. / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / ATP-dependent RNA helicase DbpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsHardin, J.W. / Hu, Y. / McKay, D.B.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif.
Authors: Hardin, J.W. / Hu, Y.X. / McKay, D.B.
#1: Journal: Rna / Year: 2006
Title: The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.
Authors: Wang, S. / Hu, Y. / Overgaard, M.T. / Karginov, F.V. / Uhlenbeck, O.C. / McKay, D.B.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: RNA (69-MER)
B: ATP-dependent RNA helicase dbpA


Theoretical massNumber of molelcules
Total (without water)32,1522
Polymers32,1522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-9 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.010, 91.63, 115.28
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (69-MER)


Mass: 23860.158 Da / Num. of mol.: 1
Fragment: E. coli 23 S ribosomal RNA (nucleotides 2508-2580 with GAAA tetraloop in nucleotides 2530-2533 and A2581 at 3' end)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein ATP-dependent RNA helicase dbpA


Mass: 8291.884 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dbpA, deaD, yxiN, BSU39110, SS8E / Production host: Escherichia coli (E. coli) / Strain (production host): BL23(DE3)
References: UniProt: P42305, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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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: 3.7 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8
Details: 20 mg/ml protein-RNA complex with RNA in 5% molar excess, 5 mM Tris-HCL, 200 mM potassium acetate, 26-30% PEG-3350, pH 8.0, VAPOR DIFFUSION, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCL11
2potassium acetate11
3PEG-335011
4Tris-HCL12
5potassium acetate12
6PEG-335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 11090 / Num. obs: 10490 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.054
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.1 % / Rsym value: 0.296 / % possible all: 71.6

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Processing

Software
NameVersionClassification
ALSBOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.902→19.896 Å / SU ML: 0.31 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1039 10.4 %10% random
Rwork0.209 ---
all0.216 11043 --
obs0.2158 9995 90.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.23 e/Å3
Refinement stepCycle: LAST / Resolution: 2.902→19.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 1473 0 0 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052221
X-RAY DIFFRACTIONf_angle_d1.063329
X-RAY DIFFRACTIONf_dihedral_angle_d20.935904
X-RAY DIFFRACTIONf_chiral_restr0.048436
X-RAY DIFFRACTIONf_plane_restr0.003164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.902-3.05490.3219920.2656899X-RAY DIFFRACTION64
3.0549-3.24550.31581600.22741185X-RAY DIFFRACTION87
3.2455-3.49490.26461610.21431309X-RAY DIFFRACTION94
3.4949-3.84430.26661540.20121324X-RAY DIFFRACTION96
3.8443-4.39530.2851420.21061368X-RAY DIFFRACTION96
4.3953-5.5180.2671660.19411400X-RAY DIFFRACTION98
5.518-19.89670.26421640.20611471X-RAY DIFFRACTION97

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