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- PDB-4xgt: Structure of RNA Helicase FRH a Critical Component of the Neurosp... -

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Basic information

Entry
Database: PDB / ID: 4xgt
TitleStructure of RNA Helicase FRH a Critical Component of the Neurospora Crassa Circadian Clock
ComponentsFRQ-interacting RNA helicase
KeywordsHYDROLASE / ATPase / circadian clock
Function / homology
Function and homology information


RNA catabolic process / maturation of 5.8S rRNA / RNA helicase activity / hydrolase activity / RNA binding / ATP binding / nucleus
Similarity search - Function
rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain ...rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / 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
FRQ-interacting RNA helicase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 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
DepositionJan 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: FRQ-interacting RNA helicase


Theoretical massNumber of molelcules
Total (without water)112,8311
Polymers112,8311
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.841, 113.462, 143.626
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 / Probable ATP dependent 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) / Gene: B9B11.040, frh, NCU03363.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q873J5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
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: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.09→143.63 Å / Num. obs: 24298 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 97.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.051 / Net I/σ(I): 12.1 / Num. measured all: 173112
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
3.09-3.267.41.31.52581134790.6070.511100
9.77-143.636.20.04532.953488640.9960.01999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1819)refinement
Aimless0.1.27data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XGJ

2xgj


Resolution: 3.09→69.113 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 1237 5.1 %Random selection
Rwork0.2318 23004 --
obs0.2351 24241 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.82 Å2 / Biso mean: 95.9639 Å2 / Biso min: 47.96 Å2
Refinement stepCycle: final / Resolution: 3.09→69.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7681 0 2218 18 9917
Biso mean--87.63 84.47 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047829
X-RAY DIFFRACTIONf_angle_d0.90310572
X-RAY DIFFRACTIONf_chiral_restr0.0341179
X-RAY DIFFRACTIONf_plane_restr0.0041374
X-RAY DIFFRACTIONf_dihedral_angle_d16.672998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0901-3.21380.39391380.340925132651100
3.2138-3.36010.34341430.310124922635100
3.3601-3.53720.38151480.302325162664100
3.5372-3.75880.38581200.267825442664100
3.7588-4.0490.36191220.258725362658100
4.049-4.45640.29311330.231425592692100
4.4564-5.10110.24251490.21325462695100
5.1011-6.42610.34061400.242725842724100
6.4261-69.13010.2271440.182714285899

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