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- PDB-6qie: Crystal structure of DEAH-box ATPase Prp43-S387G -

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Basic information

Entry
Database: PDB / ID: 6qie
TitleCrystal structure of DEAH-box ATPase Prp43-S387G
ComponentsPrp43
KeywordsHYDROLASE / Splicing / DEAH / ATPase / helicase
Function / homology
Function and homology information


RNA splicing / spliceosomal complex / mRNA processing / hydrolase activity / RNA helicase activity / RNA helicase / RNA binding / ATP binding / metal ion binding
Similarity search - Function
DHX15, DEXH-box helicase domain / : / 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. ...DHX15, DEXH-box helicase domain / : / 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 / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHamann, F. / Ficner, R. / Enders, M.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis for RNA translocation by DEAH-box ATPases.
Authors: Hamann, F. / Enders, M. / Ficner, R.
History
DepositionJan 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 3, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prp43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,52119
Polymers80,4241
Non-polymers2,09718
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-164 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.640, 102.980, 118.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prp43


Mass: 80423.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0005780 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta II / References: UniProt: G0RY84

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Non-polymers , 7 types, 57 molecules

#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES pH7, 3% PEG4000, 35% MPD

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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: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→77.848 Å / Num. obs: 30459 / % possible obs: 99.8 % / Redundancy: 9.115 % / Biso Wilson estimate: 71.307 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.119 / Χ2: 1.013 / Net I/σ(I): 14.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.89.2441.4781.6430660.6481.56699.8
2.8-39.1960.9122.5550190.8390.96799.8
3-3.29.3080.5224.3538900.9390.55299.9
3.2-3.59.2570.2877.5242800.980.304100
3.5-3.79.2120.16911.921480.9950.17899.9
3.7-4.29.0620.10817.3637250.9970.11499.7
4.2-58.9190.06825.5533100.9990.07299.3
5-69.1640.06627.2820570.9990.0799.7
6-88.7530.04935.1616800.9990.05299.9
8-108.6530.02462.5960610.02699.8
10-208.3490.01981.5658410.02199.5
20-506.30.01682.149010.01898.9
50-77.8482.750.01164.61410.01357.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTJ

5ltj


Resolution: 2.7→77.848 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.26
RfactorNum. reflection% reflection
Rfree0.2537 1522 5 %
Rwork0.2286 --
obs0.2299 30443 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 179.6 Å2 / Biso mean: 77.4803 Å2 / Biso min: 39.98 Å2
Refinement stepCycle: final / Resolution: 2.7→77.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 130 39 5741
Biso mean--99.31 66.26 -
Num. residues----703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7003-2.78740.46861350.428725832718100
2.7874-2.88710.37761350.380325772712100
2.8871-3.00260.34531360.32825802716100
3.0026-3.13930.31821370.287825932730100
3.1393-3.30480.24391380.271126242762100
3.3048-3.51190.2751370.246225982735100
3.5119-3.7830.23251390.213526402779100
3.783-4.16370.2231370.195526162753100
4.1637-4.76610.22921390.18832635277499
4.7661-6.00450.25451410.227526712812100
6.0045-77.88040.21661480.189528042952100
Refinement TLS params.Method: refined / Origin x: 2.2788 Å / Origin y: 214.0375 Å / Origin z: 41.7493 Å
111213212223313233
T0.3668 Å20.0065 Å2-0.0149 Å2-0.4844 Å20.0307 Å2--0.4363 Å2
L0.4725 °2-0.0458 °2-0.0775 °2-0.7517 °20.8328 °2--2.4438 °2
S-0.0447 Å °-0.0315 Å °-0.0157 Å °-0.0584 Å °-0.0472 Å °0.1233 Å °-0.1474 Å °-0.1678 Å °0.0841 Å °
Refinement TLS groupSelection details: (chain A and resseq 60:762)

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