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- PDB-6zwx: Crystal structure of E. coli RNA helicase HrpA -

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Basic information

Entry
Database: PDB / ID: 6zwx
TitleCrystal structure of E. coli RNA helicase HrpA
ComponentsATP-dependent RNA helicase HrpA
KeywordsRNA BINDING PROTEIN / RNA helicase / NTPase / bacterial helicase / DExH-box
Function / homology
Function and homology information


RNA modification / 3'-5' RNA helicase activity / helicase activity / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation ...RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase HrpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGrass, L.M. / Wollenhaupt, J. / Barthel, T. / Loll, B. / Wahl, M.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility.
Authors: Grass, L.M. / Wollenhaupt, J. / Barthel, T. / Parfentev, I. / Urlaub, H. / Loll, B. / Klauck, E. / Antelmann, H. / Wahl, M.C.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 4, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase HrpA


Theoretical massNumber of molelcules
Total (without water)86,8871
Polymers86,8871
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.127, 116.544, 92.591
Angle α, β, γ (deg.)90.000, 98.615, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein ATP-dependent RNA helicase HrpA


Mass: 86887.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hrpA, b1413, JW5905 / Production host: Escherichia coli (E. coli) / References: UniProt: P43329, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 9 % [w/v] PEG 400, 0.2 M NaCl, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.7→49.249 Å / Num. obs: 23139 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 84.82 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3427 / CC1/2: 0.56 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.16 Å / SU ML: 0.4391 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.6411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2763 1157 5.01 %
Rwork0.2209 21954 -
obs0.2235 23111 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5901 0 0 11 5912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376006
X-RAY DIFFRACTIONf_angle_d0.6178116
X-RAY DIFFRACTIONf_chiral_restr0.0421914
X-RAY DIFFRACTIONf_plane_restr0.00551058
X-RAY DIFFRACTIONf_dihedral_angle_d13.65032324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.39461440.3692684X-RAY DIFFRACTION98.92
2.82-2.970.37461440.31772739X-RAY DIFFRACTION99.86
2.97-3.160.35761430.31482744X-RAY DIFFRACTION99.83
3.16-3.40.32941440.27882732X-RAY DIFFRACTION99.86
3.4-3.740.30781440.2452752X-RAY DIFFRACTION99.9
3.74-4.290.28721440.21492747X-RAY DIFFRACTION99.97
4.29-5.40.24051460.19252754X-RAY DIFFRACTION100
5.4-49.160.23811480.18642802X-RAY DIFFRACTION99.8
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)
11.526855770710.04787631764110.6553753594292.78261383394-0.5282040640732.98326139374-0.125976873289-0.201379037540.22358449670.6989989442220.151160048431-0.170427481704-0.788094255199-0.3883008432860.1788693285510.8666385389590.1646528761990.1967996075730.797570571992-0.0001433209660740.583414322434-18.5601743853-0.37229431448313.6316099414
20.986542016127-0.670238124434-0.01360432871572.746535132350.01850875282811.24667000397-0.167011306643-0.05357151354890.5050241437970.277384214690.230771109690.21745868169-0.1466657193030.118361624179-0.01229817663640.5064613719540.10868527523-0.07434053277740.684114946538-0.02122416626670.795372997965-20.139935133718.0571219642-14.9165155545
31.34789903065-1.07290160101-0.08819287283072.154422947140.8230366538731.587100851660.00165193895050.1103769290870.0677853835481-0.4272535635790.0612770738247-0.1992919968410.2836055617480.1252521076350.002898825985540.6880256804440.110594613055-0.08881919667790.651354774286-0.05755481169430.639821260589-8.34192606-11.7368897852-31.1131295545
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 248 )6 - 2481 - 243
22chain 'A' and (resid 249 through 443 )249 - 443244 - 433
33chain 'A' and (resid 444 through 756 )444 - 756434 - 736

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