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- PDB-2hjv: Structure of the second domain (residues 207-368) of the Bacillus... -

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Basic information

Entry
Database: PDB / ID: 2hjv
TitleStructure of the second domain (residues 207-368) of the Bacillus subtilis YxiN protein
ComponentsATP-dependent RNA helicase dbpA
KeywordsHYDROLASE / parallel alpha-beta
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. / 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 ...ATP-dependent RNA helicase DbpA / DEAD box helicase DbpA/CsdA, RNA-binding domain / DbpA RNA binding 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 nucleotide triphosphate hydrolases / Nucleotide-binding alpha-beta plait domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DbpA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMcKay, D.B. / Caruthers, J.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN.
Authors: Caruthers, J.M. / Hu, Y. / McKay, D.B.
History
DepositionJul 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / 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: ATP-dependent RNA helicase dbpA
B: ATP-dependent RNA helicase dbpA


Theoretical massNumber of molelcules
Total (without water)37,3522
Polymers37,3522
Non-polymers00
Water2,936163
1
A: ATP-dependent RNA helicase dbpA


Theoretical massNumber of molelcules
Total (without water)18,6761
Polymers18,6761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase dbpA


Theoretical massNumber of molelcules
Total (without water)18,6761
Polymers18,6761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.20, 105.20, 66.03
Angle α, β, γ (deg.)90., 90., 120.
Int Tables number169
Space group name H-MP61

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Components

#1: Protein ATP-dependent RNA helicase dbpA


Mass: 18676.176 Da / Num. of mol.: 2
Fragment: Bacillus subtilis YxiN domain 2 (Residues 207-368)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dbpA / Plasmid: pTWIN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P42305, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Precipitant: 3% PEG-MME 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2004
RadiationMonochromator: double crystal, Si(1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 30262 / Num. obs: 27397 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.069
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.3 % / Rsym value: 0.227 / % possible all: 95.9

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homologous domain of eIF4A (PDB 1FUK)

1fuk


Resolution: 1.95→30.53 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 866412.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1600 5.9 %RANDOM
Rwork0.209 ---
obs0.209 26991 88.7 %-
all-26991 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2894 Å2 / ksol: 0.368646 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å22.93 Å20 Å2
2--1.75 Å20 Å2
3----3.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.95→30.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 0 163 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.732.5
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.227 169 6.3 %
Rwork0.221 2495 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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