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- PDB-7akp: Crystal structure of E. coli RNA helicase HrpA-D305A -

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Basic information

Entry
Database: PDB / ID: 7akp
TitleCrystal structure of E. coli RNA helicase HrpA-D305A
ComponentsATP-dependent RNA helicase HrpA
KeywordsRNA BINDING PROTEIN / RNA helicase / NTPase / bacterial helicase / DExH-box
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / RNA helicase / ATP binding
Similarity search - Function
RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / 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 ...RNA helicase HrpA / RNA helicase HrpA, C-terminal / Domain of unknown function (DUF3418) / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.59 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
DepositionOct 1, 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 1.3Jan 31, 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 HrpA


Theoretical massNumber of molelcules
Total (without water)89,7861
Polymers89,7861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.894, 114.902, 94.614
Angle α, β, γ (deg.)90.000, 101.937, 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 / ATP-dependent RNA helicase HrpB / ATP-dependent helicase / ATP-dependent helicase HrpA / Putative ...ATP-dependent RNA helicase HrpB / ATP-dependent helicase / ATP-dependent helicase HrpA / Putative ATP-dependent helicase


Mass: 89785.781 Da / Num. of mol.: 1 / Mutation: D305A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: hrpA, hrpB_2, ACU57_01855, AUQ13_00250, BANRA_00811, BANRA_04135, BMA87_16915, BUE81_10335, BvCms2454_02596, BvCmsHHP001_04653, C5N07_19950, C9Z39_02430, CA593_20890, CI694_27345, CIG45_23500, ...Gene: hrpA, hrpB_2, ACU57_01855, AUQ13_00250, BANRA_00811, BANRA_04135, BMA87_16915, BUE81_10335, BvCms2454_02596, BvCmsHHP001_04653, C5N07_19950, C9Z39_02430, CA593_20890, CI694_27345, CIG45_23500, D0X26_25730, D3821_04265, D9G69_18360, D9J52_23225, DBQ99_13815, DJ503_20330, DL326_20175, DT034_20065, E2119_23590, E4K55_22820, E4K60_22175, E4K61_19375, EA213_21160, EC3234A_28c00370, EC3426_02431, EEP23_09730, EI021_18420, EI028_21745, EI041_18575, ELT20_16685, EPT01_12920, EYD11_11805, FV293_21585, GHR40_16525, GKF86_19260, GKF89_18325, GP689_04140, GQM17_20230, NCTC12650_02980, NCTC9062_00712, PGD_01858, RK56_010590, SAMEA3472080_03366, SAMEA3752559_04937, SK85_01607
Production host: Escherichia coli (E. coli) / References: UniProt: A0A024L2B5, RNA helicase

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 7 % PEG 3350, 0.05 M HEPES, pH 7, 0.1 M potassium chloride, 0.01 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.59→48.81 Å / Num. obs: 25697 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.987 / Net I/σ(I): 7.27
Reflection shellResolution: 2.59→2.75 Å / Num. unique obs: 4048 / CC1/2: 0.333

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZWX

6zwx


Resolution: 2.59→48.81 Å / Cross valid method: FREE R-VALUE / σ(F): 165.93 / Phase error: 39.6277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 1292 5.03 %
Rwork0.2109 24404 -
obs0.2195 25696 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.52 Å2
Refinement stepCycle: LAST / Resolution: 2.59→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 0 0 5800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345902
X-RAY DIFFRACTIONf_angle_d0.61497969
X-RAY DIFFRACTIONf_chiral_restr0.0414893
X-RAY DIFFRACTIONf_plane_restr0.00491039
X-RAY DIFFRACTIONf_dihedral_angle_d14.23842286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.70.32431390.3122653X-RAY DIFFRACTION91.29
2.7-2.820.32431410.29452672X-RAY DIFFRACTION94.32
2.82-2.970.32031420.29232704X-RAY DIFFRACTION94.41
2.97-3.160.2831420.27092700X-RAY DIFFRACTION94.6
3.16-3.40.28841440.25962723X-RAY DIFFRACTION94.71
3.4-3.740.27431420.22912698X-RAY DIFFRACTION94.83
3.74-4.280.2171440.19732744X-RAY DIFFRACTION94.85
4.28-5.40.19761440.16972734X-RAY DIFFRACTION94.86
5.4-48.810.22291470.18582783X-RAY DIFFRACTION94.92
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)
10.01388603891010.0124437356990.00403071651370.01941368984990.006534718262310.002988255637040.0001567021763-0.00476989197259-0.005464187836880.00697724914171-0.00249062891237-0.02715330734120.02236979240280.006046686391210.0108875471290.4062399206660.0203778684897-0.05154819809460.122051409978-0.03355658884190.476591075391-5.26064733425-0.19128085054860.2334173183
20.0107573761203-0.005742174771260.005147674034610.00715752487922-0.0006880890627140.003214611367140.00971313025967-0.00111528882230.000157943771814-0.00508974580783-0.005265511839320.004503721250340.03834772422680.005040202330530.01650939466320.4340111269770.0358385036999-0.08428269515060.138280576040.005873768097920.516491753105-9.2992339517412.579890604531.9327739574
30.01427347299090.00014152082189-0.001032049580340.0195045889055-0.005502751721090.0178925201831-0.01203627765620.003429935772480.0310616612437-0.00577947035637-0.000191922894817-0.0125094837049-0.00311130054550.00376684243211-0.03397871265730.3626043248960.0257874313873-0.1313518378190.1343134301060.01120749951650.4974057868985.61077787126-11.795864109513.5175889785
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 7 through 229 )7 - 2291 - 220
22chain 'A' and (resid 230 through 471 )230 - 471221 - 448
33chain 'A' and (resid 472 through 751 )472 - 751449 - 723

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