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- PDB-8po6: Structure of Escherichia coli HrpA apo form -

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Basic information

Entry
Database: PDB / ID: 8po6
TitleStructure of Escherichia coli HrpA apo form
ComponentsATP-dependent RNA helicase HrpA
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
PHOSPHATE ION / ATP-dependent RNA helicase HrpA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 China
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase HrpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4092
Polymers86,3141
Non-polymers951
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-7 kcal/mol
Surface area35860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.605, 114.897, 94.011
Angle α, β, γ (deg.)90.000, 100.857, 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: 86313.797 Da / Num. of mol.: 1
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: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Hepes 7% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.656→92.328 Å / Num. obs: 23640 / % possible obs: 99 % / Redundancy: 6.3 % / Biso Wilson estimate: 55.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.656→2.702 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2 / Num. unique obs: 1051 / CC1/2: 0.891 / Rpim(I) all: 0.314 / Rrim(I) all: 0.669 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.17rc5_3630refinement
PHENIX1.17rc5_3630refinement
SORTAVBUILT 20190315data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→29.73 Å / SU ML: 0.4653 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.5545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 1122 4.75 %
Rwork0.2062 22478 -
obs0.2086 23600 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.75 Å2
Refinement stepCycle: LAST / Resolution: 2.66→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6031 0 5 36 6072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286143
X-RAY DIFFRACTIONf_angle_d0.60338308
X-RAY DIFFRACTIONf_chiral_restr0.043932
X-RAY DIFFRACTIONf_plane_restr0.00361090
X-RAY DIFFRACTIONf_dihedral_angle_d18.10122378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.780.491250.38332606X-RAY DIFFRACTION92.39
2.78-2.920.38571600.29392781X-RAY DIFFRACTION99.26
2.92-3.110.32831400.27012853X-RAY DIFFRACTION99.87
3.11-3.350.30331310.26982826X-RAY DIFFRACTION99.86
3.35-3.680.25251380.22062837X-RAY DIFFRACTION99.93
3.68-4.210.25091450.19562835X-RAY DIFFRACTION99.97
4.21-5.30.221440.16412855X-RAY DIFFRACTION99.97
5.3-29.730.19391390.15632885X-RAY DIFFRACTION99.74
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)
12.15012046703-1.029074730081.002211038593.73729540812-0.4494064246626.07885182-0.00734380660453-0.2157793430790.1562009611950.5212418406230.0533507905715-0.344114772978-0.256455426939-0.457003161913-0.02501262422220.385778112066-0.02520859756030.005394512579230.365594158382-0.02397182107010.43698315496214.857423163634.526988160259.8935984553
22.0488193959-0.8523335535290.7848875139124.46003528351-1.89612057431.72445298471-0.139172321421-0.2234009402010.4677551195090.3332063137210.0430659274748-0.267085987676-0.3617674913980.002833160075520.05275031183450.5231071714420.12358756819-0.05012612372440.459084909283-0.1619642161230.45778386358512.290447149448.346073823330.4237395264
31.5503024747-1.241297704410.7110040197316.93100268294-0.5042163832591.606350950850.04703032605290.02524924296020.0462557104876-0.2023903918-0.05437783808820.01227688066730.1341814191570.05418870274530.007203356182140.3259759742610.0616177330495-0.006920469297750.3712794702080.0002911456560420.33574623474426.199294890521.825023127713.3818451329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 471 )
3X-RAY DIFFRACTION3chain 'A' and (resid 472 through 758 )

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