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- PDB-8po7: Structure of Escherichia coli HrpA in complex with ADP and dinucl... -

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Basic information

Entry
Database: PDB / ID: 8po7
TitleStructure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC
Components
  • ATP-dependent RNA helicase HrpA
  • DNA (5'-D(P*CP*C)-3')
KeywordsHYDROLASE / Helicase
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / DNA / ATP-dependent RNA helicase HrpA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsXin, B.G. / Yuan, L.G. / Zhang, L.L. / Xie, S.M. / Liu, N.N. / Ai, X. / Li, H.H. / Rety, S. / Xi, X.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870788 China
Other governmentZ101021903
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.
Authors: Xin, B.G. / Huang, L.Y. / Yuan, L.G. / Liu, N.N. / Li, H.H. / Ai, X. / Lei, D.S. / Hou, X.M. / Rety, S. / Xi, X.G.
History
DepositionJul 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase HrpA
B: ATP-dependent RNA helicase HrpA
C: DNA (5'-D(P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,1598
Polymers173,1613
Non-polymers9985
Water10,503583
1
B: ATP-dependent RNA helicase HrpA
hetero molecules

A: ATP-dependent RNA helicase HrpA
C: DNA (5'-D(P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,1598
Polymers173,1613
Non-polymers9985
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)80.470, 106.124, 178.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein ATP-dependent RNA helicase HrpA


Mass: 86313.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hrpA, b1413, JW5905 / Plasmid: pET15b-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): C2566H / References: UniProt: P43329, RNA helicase
#2: DNA chain DNA (5'-D(P*CP*C)-3')


Mass: 533.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 588 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03M NaNO3 0.03M Na2HPO4 0.03L (NH4)2SO4 0.1M MES-Imidazole 20% ethylene glycol 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.257→91.19 Å / Num. obs: 70047 / % possible obs: 96.6 % / Redundancy: 13 % / Biso Wilson estimate: 28.45 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.063 / Rrim(I) all: 0.228 / Net I/σ(I): 15.5
Reflection shellResolution: 2.257→2.295 Å / Rmerge(I) obs: 1.71 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3566 / CC1/2: 0.807 / Rpim(I) all: 0.476 / Rrim(I) all: 1.776 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSBUILT 20180409data reduction
Aimless0.7.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→89.14 Å / SU ML: 0.2341 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.0453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 3466 4.95 %
Rwork0.1897 66575 -
obs0.1918 70041 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.71 Å2
Refinement stepCycle: LAST / Resolution: 2.26→89.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9383 39 61 583 10066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00859633
X-RAY DIFFRACTIONf_angle_d1.186113033
X-RAY DIFFRACTIONf_chiral_restr0.06281481
X-RAY DIFFRACTIONf_plane_restr0.00731697
X-RAY DIFFRACTIONf_dihedral_angle_d19.18663756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.29421480.24142670X-RAY DIFFRACTION99.51
2.29-2.320.2371570.22552702X-RAY DIFFRACTION99.97
2.32-2.350.25791570.20992714X-RAY DIFFRACTION100
2.35-2.390.23371410.21082717X-RAY DIFFRACTION100
2.39-2.430.27551200.20842750X-RAY DIFFRACTION99.93
2.43-2.470.22961380.20572750X-RAY DIFFRACTION100
2.47-2.520.26421250.1992732X-RAY DIFFRACTION100
2.52-2.570.24341870.20372667X-RAY DIFFRACTION100
2.57-2.620.29761380.2122728X-RAY DIFFRACTION99.97
2.62-2.650.2457880.22741676X-RAY DIFFRACTION95.77
2.68-2.740.2871410.20262702X-RAY DIFFRACTION99.93
2.74-2.810.27071290.20032766X-RAY DIFFRACTION100
2.81-2.880.25861410.20042755X-RAY DIFFRACTION100
2.88-2.970.26511470.18962742X-RAY DIFFRACTION100
2.97-3.060.22431530.1942706X-RAY DIFFRACTION99.51
3.06-3.170.24981420.20082747X-RAY DIFFRACTION99.93
3.17-3.30.2871310.20782762X-RAY DIFFRACTION100
3.3-3.420.22411150.20122257X-RAY DIFFRACTION99.5
3.46-3.630.23841310.18282649X-RAY DIFFRACTION99.82
3.63-3.860.21831300.17782467X-RAY DIFFRACTION88.73
3.86-4.160.22771270.16732492X-RAY DIFFRACTION89.66
4.16-4.570.15421520.15212786X-RAY DIFFRACTION100
4.57-5.240.18021440.16052805X-RAY DIFFRACTION99.86
5.24-6.60.2311490.20332838X-RAY DIFFRACTION99.5
6.6-89.140.20711350.18052995X-RAY DIFFRACTION99.71

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