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- PDB-6heg: Crystal structure of Escherichia coli DEAH/RHA helicase HrpB -

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Basic information

Entry
Database: PDB / ID: 6heg
TitleCrystal structure of Escherichia coli DEAH/RHA helicase HrpB
ComponentsATP-dependent RNA helicase HrpB
KeywordsHYDROLASE / DEAH/RHA Helicase RNA helicase
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / RNA helicase activity / single-stranded RNA binding / RNA helicase / ATP hydrolysis activity / ATP binding
Similarity search - Function
ATP-dependent helicase HrpB / ATP-dependent RNA helicase HrpB, C-terminal / ATP-dependent helicase C-terminal / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...ATP-dependent helicase HrpB / ATP-dependent RNA helicase HrpB, C-terminal / ATP-dependent helicase C-terminal / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / PHOSPHATE ION / ATP-dependent RNA helicase HrpB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.019 Å
AuthorsXin, B.G. / Chen, W.F. / Rety, S. / Dai, Y.X. / Xi, X.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370798, 11574252, 11774407 China
Chinese Academy of SciencesG-quadruplex HELI China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of Escherichia coli DEAH/RHA helicase HrpB.
Authors: Xin, B.G. / Chen, W.F. / Rety, S. / Dai, Y.X. / Xi, X.G.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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 HrpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3489
Polymers89,2481
Non-polymers1,1008
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-27 kcal/mol
Surface area37420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.550, 106.372, 180.005
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: Protein ATP-dependent RNA helicase HrpB


Mass: 89247.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hrpB, yadO, b0148, JW0144
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37024, RNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4

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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: 2.55 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: Na Citrate 0.12M PEG 2000 MME 20% (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.019→53.1942 Å / Num. obs: 19075 / % possible obs: 99.89 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 65.88 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1844 / Rpim(I) all: 0.07963 / Rrim(I) all: 0.2013 / Net I/σ(I): 8.16
Reflection shellResolution: 3.019→3.127 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.7887 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1863 / CC1/2: 0.777 / Rpim(I) all: 0.3396 / Rrim(I) all: 0.8601 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
XDSBUILT 20180409data reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XAU

2xau


Resolution: 3.019→53.186 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 946 4.96 %5%
Rwork0.2078 ---
obs0.2106 19068 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.019→53.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6061 0 62 0 6123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066219
X-RAY DIFFRACTIONf_angle_d1.0318446
X-RAY DIFFRACTIONf_dihedral_angle_d14.5163829
X-RAY DIFFRACTIONf_chiral_restr0.048968
X-RAY DIFFRACTIONf_plane_restr0.0061100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0193-3.17850.3691320.27762529X-RAY DIFFRACTION100
3.1785-3.37760.32791510.24982507X-RAY DIFFRACTION100
3.3776-3.63830.34051180.24942575X-RAY DIFFRACTION100
3.6383-4.00430.30711150.20662587X-RAY DIFFRACTION100
4.0043-4.58350.24931370.17892569X-RAY DIFFRACTION100
4.5835-5.77360.211320.18742624X-RAY DIFFRACTION100
5.7736-53.19420.22121610.1962731X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.024-0.3626-0.38671.51420.08951.86950.1273-0.01720.0166-0.0986-0.1384-0.0176-0.376-0.005100.2746-0.0028-0.01240.21550.00420.184246.077857.4282103.9458
20.451-0.0409-0.52430.6123-0.18921.56840.10420.01150.029-0.064-0.0406-0.09330.048-0.035400.224-0.02150.00040.24580.01820.223756.53939.983595.7067
30.7070.03310.64760.9060.60651.3160.0811-0.313-0.0338-0.1129-0.191-0.3219-0.1473-0.1079-0.13860.2171-0.0415-0.02440.30310.14040.387271.060236.2899118.4809
41.01850.64070.09010.6750.18710.0735-0.31760.0552-0.162-0.06880.0870.17670.03780.1376-0.02150.3597-0.04710.03110.3360.10480.430738.9493-2.4626121.9738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 175 )
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 414 )
3X-RAY DIFFRACTION3chain 'A' and (resid 415 through 558 )
4X-RAY DIFFRACTION4chain 'A' and (resid 559 through 792 )

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