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- PDB-6eud: Crystal structure of E. coli DExH-box NTPase HrpB -

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Basic information

Entry
Database: PDB / ID: 6eud
TitleCrystal structure of E. coli DExH-box NTPase HrpB
ComponentsATP-dependent RNA helicase HrpB
KeywordsRNA BINDING PROTEIN / HrpB / DEAH/RHA helicase / bacterial 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
ATP-dependent RNA helicase HrpB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsPietrzyk-Brzezinska, A.J. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationPOL 1161176 STP Germany
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of the Escherichia coli DExH-Box NTPase HrpB.
Authors: Pietrzyk-Brzezinska, A.J. / Absmeier, E. / Klauck, E. / Wen, Y. / Antelmann, H. / Wahl, M.C.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 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: ATP-dependent RNA helicase HrpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6453
Polymers89,5211
Non-polymers1242
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint5 kcal/mol
Surface area38460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.710, 131.410, 166.110
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: 89521.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hrpB, yadO, b0148, JW0144 / Production host: Escherichia coli (E. coli) / References: UniProt: P37024, RNA helicase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES-NaOH, pH 6.5, 5% [w/v] PEG 6000, 10 % [v/v] MPD, 0.1 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763, 0.9795
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97951
ReflectionResolution: 2.4→48 Å / Num. obs: 43551 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 3189 / CC1/2: 0.584 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.623 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.2386 2138 4.91 %
Rwork0.1877 --
obs0.1903 43549 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 8 308 6557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086370
X-RAY DIFFRACTIONf_angle_d1.0878651
X-RAY DIFFRACTIONf_dihedral_angle_d13.5942444
X-RAY DIFFRACTIONf_chiral_restr0.041994
X-RAY DIFFRACTIONf_plane_restr0.0051142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45580.31091370.28012728X-RAY DIFFRACTION100
2.4558-2.51720.3141370.26832723X-RAY DIFFRACTION100
2.5172-2.58530.34961410.25752702X-RAY DIFFRACTION100
2.5853-2.66130.33681270.24082724X-RAY DIFFRACTION100
2.6613-2.74720.27481450.23842750X-RAY DIFFRACTION100
2.7472-2.84540.28611400.23832705X-RAY DIFFRACTION100
2.8454-2.95930.31521330.23242723X-RAY DIFFRACTION100
2.9593-3.0940.3121580.22762729X-RAY DIFFRACTION100
3.094-3.2570.2841150.19842783X-RAY DIFFRACTION100
3.257-3.46110.23991540.192735X-RAY DIFFRACTION100
3.4611-3.72820.23191320.17562752X-RAY DIFFRACTION100
3.7282-4.10320.21061480.15452795X-RAY DIFFRACTION100
4.1032-4.69650.1991520.14612774X-RAY DIFFRACTION100
4.6965-5.91530.21631390.16682828X-RAY DIFFRACTION100
5.9153-47.63260.181800.15972960X-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)
12.84490.2521-0.00743.5431-2.72416.6584-0.067-0.4619-0.74660.3288-0.281-0.02392.07080.52790.24491.1220.03680.08620.61730.07840.5654-3.1381-3.328179.9537
20.4682-0.0359-0.48960.38520.73292.1809-0.01090.0466-0.12740.0376-0.04230.02490.2151-0.22440.03110.2943-0.0176-0.02640.26870.01770.31187.611715.316874.1922
32.2445-1.55390.53952.4167-0.4030.83370.09510.14020.2495-0.0523-0.0428-0.2772-0.0784-0.0086-0.06210.3084-0.02030.02320.24670.05550.3261-8.566348.591445.3927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -2:129)
2X-RAY DIFFRACTION2(chain A and resid 130:519)
3X-RAY DIFFRACTION3(chain A and resid 520:805)

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