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- PDB-8cnt: Structure of the DEAH-box helicase Prp16 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8cnt
TitleStructure of the DEAH-box helicase Prp16 in complex with ADP
ComponentsPre-mRNA splicing factor ATP-dependent RNA helicase prp16-like protein
KeywordsHYDROLASE / DEAH-box helicase
Function / homology
Function and homology information


helicase activity / nucleic acid binding / hydrolase activity / ribonucleoprotein complex / ATP binding
Similarity search - Function
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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain ...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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Pre-mRNA splicing factor ATP-dependent RNA helicase prp16-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGarbers, T.B. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 860, TP A02 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of Prp16 in complex with ADP.
Authors: Garbers, T.B. / Enders, M. / Neumann, P. / Ficner, R.
History
DepositionFeb 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA splicing factor ATP-dependent RNA helicase prp16-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2654
Polymers71,5311
Non-polymers7343
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area26900 Å2
Unit cell
Length a, b, c (Å)55.130, 102.140, 106.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pre-mRNA splicing factor ATP-dependent RNA helicase prp16-like protein


Mass: 71531.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0009880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0S0F9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5 0.005 M Magnesiumchloride 20 % PEG 4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→48.97 Å / Num. obs: 91538 / % possible obs: 99.9 % / Redundancy: 7.07 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.115 / Net I/σ(I): 11.78
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.9-21.562130120.5031.6861
2-2.11.018106820.6921.0981
2.1-2.30.601162110.8580.6491
2.3-80.072504100.9990.0781
8-140.04110020.9990.0441
14-170.039980.9980.0431
17-500.0391230.9980.0441

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.973 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23819 2409 5 %RANDOM
Rwork0.19295 ---
obs0.19527 45747 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.984 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 47 423 5396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135072
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154856
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6496867
X-RAY DIFFRACTIONr_angle_other_deg1.3331.57611192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27621.692266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66915900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6911539
X-RAY DIFFRACTIONr_chiral_restr0.0690.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021140
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6663.5712479
X-RAY DIFFRACTIONr_mcbond_other2.6643.5692478
X-RAY DIFFRACTIONr_mcangle_it3.6235.3443097
X-RAY DIFFRACTIONr_mcangle_other3.6235.3463098
X-RAY DIFFRACTIONr_scbond_it3.6644.1442593
X-RAY DIFFRACTIONr_scbond_other3.6634.1452594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6046.013771
X-RAY DIFFRACTIONr_long_range_B_refined7.31443.4215760
X-RAY DIFFRACTIONr_long_range_B_other7.28743.1755686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 173 -
Rwork0.321 3280 -
obs--99.88 %

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