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- PDB-5dzr: Structure of RNA Helicase FRH a Critical Component of the Neurosp... -

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Basic information

Entry
Database: PDB / ID: 5dzr
TitleStructure of RNA Helicase FRH a Critical Component of the Neurospora Crassa Circadian Clock
ComponentsFRQ-interacting RNA helicase
KeywordsHYDROLASE / helicase / circadian clock / RNA BINDING PROTEIN
Function / homology
Function and homology information


TRAMP complex / RNA catabolic process / maturation of 5.8S rRNA / RNA helicase activity / hydrolase activity / RNA binding / ATP binding
Similarity search - Function
Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT ...Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FRQ-interacting RNA helicase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.161 Å
AuthorsConrad, K.S. / Crane, B.C.
CitationJournal: Embo J. / Year: 2016
Title: Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock.
Authors: Conrad, K.S. / Hurley, J.M. / Widom, J. / Ringelberg, C.S. / Loros, J.J. / Dunlap, J.C. / Crane, B.R.
History
DepositionSep 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FRQ-interacting RNA helicase


Theoretical massNumber of molelcules
Total (without water)112,8311
Polymers112,8311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.7970, 107.7490, 125.7690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FRQ-interacting RNA helicase


Mass: 112830.938 Da / Num. of mol.: 1 / Fragment: residues 114-1106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: frh, NCU03363 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1K502

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: sodium citrate, PEG600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.16→125.77 Å / Num. obs: 18063 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 92.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.08 / Net I/σ(I): 9.6 / Num. measured all: 71555
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.16-3.333.81.4381.2978125530.6480.82696.9
10-125.773.70.02640.524266580.9990.01598.1

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGT

4xgt


Resolution: 3.161→81.826 Å / SU ML: 0.61 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 37.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3252 909 5.09 %
Rwork0.2635 16956 -
obs0.2664 17865 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.7 Å2 / Biso mean: 92.2313 Å2 / Biso min: 46.15 Å2
Refinement stepCycle: final / Resolution: 3.161→81.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 2230 0 7697
Biso mean--86.83 --
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037844
X-RAY DIFFRACTIONf_angle_d0.76710593
X-RAY DIFFRACTIONf_chiral_restr0.0291183
X-RAY DIFFRACTIONf_plane_restr0.0041377
X-RAY DIFFRACTIONf_dihedral_angle_d13.2973002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1612-3.35920.4611520.40092652280493
3.3592-3.61860.38231600.33632768292897
3.6186-3.98270.35991590.29042833299298
3.9827-4.5590.31751350.26122814294996
4.559-5.74370.35041630.2592858302198
5.7437-81.85360.24171400.21493031317198

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