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- PDB-6qws: Crystal structure of the Ski2 RNA-helicase Brr2 from Chaetomium t... -

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Basic information

Entry
Database: PDB / ID: 6qws
TitleCrystal structure of the Ski2 RNA-helicase Brr2 from Chaetomium thermophilum in the apo state
ComponentsPre-mRNA splicing helicase-like protein
KeywordsRNA BINDING PROTEIN / Helicase Brr2 Ski2 Chaetomium thermophilum splicing RNA
Function / homology
Function and homology information


helicase activity / mRNA processing / nucleic acid binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily ...Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / Sec63 domain / Sec63 Brl domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pre-mRNA splicing helicase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAbsmeier, E. / Santos, K.F. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Structure / Year: 2020
Title: Molecular Mechanism Underlying Inhibition of Intrinsic ATPase Activity in a Ski2-like RNA Helicase.
Authors: Absmeier, E. / Santos, K.F. / Wahl, M.C.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Pre-mRNA splicing helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,0197
Polymers196,4421
Non-polymers5766
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-95 kcal/mol
Surface area73750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.520, 124.520, 128.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Pre-mRNA splicing helicase-like protein


Mass: 196442.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0009470 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S0B9
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl, PEG 3350, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 33329 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.98 / Rrim(I) all: 0.27 / Net I/σ(I): 7.38
Reflection shellResolution: 3.3→3.39 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 2454 / CC1/2: 0.37 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M59

5m59


Resolution: 3.3→44.63 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.49
RfactorNum. reflection% reflection
Rfree0.2615 1975 5.93 %
Rwork0.2063 --
obs0.2096 33291 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13463 0 30 2 13495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313783
X-RAY DIFFRACTIONf_angle_d0.56818694
X-RAY DIFFRACTIONf_dihedral_angle_d16.0358376
X-RAY DIFFRACTIONf_chiral_restr0.0422105
X-RAY DIFFRACTIONf_plane_restr0.0042392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.38260.37561470.32162237X-RAY DIFFRACTION100
3.3826-3.47410.3761340.29792251X-RAY DIFFRACTION100
3.4741-3.57620.3421400.2842234X-RAY DIFFRACTION100
3.5762-3.69160.33531460.2582235X-RAY DIFFRACTION100
3.6916-3.82350.34981400.24042213X-RAY DIFFRACTION100
3.8235-3.97650.29131500.23482274X-RAY DIFFRACTION100
3.9765-4.15730.27351400.2192242X-RAY DIFFRACTION100
4.1573-4.37630.24921430.19782207X-RAY DIFFRACTION100
4.3763-4.65030.2211350.18212261X-RAY DIFFRACTION100
4.6503-5.00890.22791460.17432239X-RAY DIFFRACTION100
5.0089-5.51210.2261290.18552219X-RAY DIFFRACTION100
5.5121-6.30780.2521520.20622257X-RAY DIFFRACTION100
6.3078-7.93990.24191420.19292223X-RAY DIFFRACTION100
7.9399-44.63440.19351310.1452224X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -100.5067 Å / Origin y: 184.4708 Å / Origin z: -16.2077 Å
111213212223313233
T0.4603 Å2-0.014 Å20.0544 Å2-0.5923 Å20.0776 Å2--0.586 Å2
L0.4914 °2-0.0179 °2-0.0798 °2-0.3231 °2-0.1146 °2--1.3229 °2
S-0.0009 Å °0.0382 Å °-0.043 Å °0.0949 Å °0.0723 Å °0.1058 Å °0.1543 Å °-0.5293 Å °-0.0322 Å °
Refinement TLS groupSelection details: all

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