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- PDB-6qid: Crystal structure of DEAH-box ATPase Prp43-S387A -

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Basic information

Entry
Database: PDB / ID: 6qid
TitleCrystal structure of DEAH-box ATPase Prp43-S387A
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DI(HYDROXYETHYL)ETHER / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.204 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

Downloads & links

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Assembly

Deposited unit
A: Prp43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,83724
Polymers80,4381
Non-polymers2,39923
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-175 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.820, 105.450, 119.230
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: 80437.961 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 , 8 types, 727 molecules

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


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 704 / 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: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES pH 7, 3% PEG4000, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.2→35.614 Å / Num. obs: 57004 / % possible obs: 99.1 % / Redundancy: 7.474 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Χ2: 1.076 / Net I/σ(I): 20.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.34.1980.5662.5165870.8190.64693
2.3-2.45.10.4483.6359740.9070.5100
2.4-2.65.4780.3165.2493400.9490.35100
2.6-2.86.0120.2237.7968880.9770.244100
2.8-3.16.650.13912.6673160.9920.151100
3.1-3.68.0550.07624.5774050.9980.081100
3.6-4.29.8640.04641.5549030.9990.049100
4.2-512.4280.03658.88343710.038100
5-615.5030.0459.97212010.041100
6-815.0020.03566.51171710.036100
8-1014.1880.02293.4663310.022100
10-2012.6620.01996.8260010.019100
20-508.9880.0271.278410.02291.3
35.614-50

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Processing

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

5ltj


Resolution: 2.204→35.614 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 2850 5 %
Rwork0.1836 54135 -
obs0.1849 56985 99.66 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.01 Å2 / Biso mean: 36.912 Å2 / Biso min: 13.53 Å2
Refinement stepCycle: final / Resolution: 2.204→35.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5601 0 149 704 6454
Biso mean--68.2 45.88 -
Num. residues----703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2041-2.24210.28291330.27022515264894
2.2421-2.28290.25861410.247726792820100
2.2829-2.32680.28121400.230426582798100
2.3268-2.37420.26341420.231827022844100
2.3742-2.42590.24941400.21626682808100
2.4259-2.48230.25941430.217527022845100
2.4823-2.54430.24381410.212626792820100
2.5443-2.61310.23251420.209426982840100
2.6131-2.690.2691400.200826732813100
2.69-2.77680.21761430.203827062849100
2.7768-2.8760.24911410.200626892830100
2.876-2.99110.23151430.194927172860100
2.9911-3.12710.21091420.195726952837100
3.1271-3.29190.22861430.185427212864100
3.2919-3.49790.19111430.17527132856100
3.4979-3.76780.18481430.156427202863100
3.7678-4.14640.15751450.149827432888100
4.1464-4.74520.1611450.145227552900100
4.7452-5.97390.20271470.16728022949100
5.9739-35.61880.17631530.177129003053100
Refinement TLS params.Method: refined / Origin x: 1.8609 Å / Origin y: 218.868 Å / Origin z: 41.6579 Å
111213212223313233
T0.1456 Å2-0.0053 Å2-0.0096 Å2-0.1191 Å2-0.0066 Å2--0.1816 Å2
L0.1864 °20.0191 °20.036 °2-0.3346 °20.4257 °2--1.3001 °2
S0.005 Å °0.0111 Å °-0.0138 Å °0.0083 Å °0.013 Å °-0.0111 Å °0.0005 Å °0.0387 Å °-0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA60 - 762
2X-RAY DIFFRACTION1allA1301 - 2601
3X-RAY DIFFRACTION1allA2701 - 2901
4X-RAY DIFFRACTION1allA3001
5X-RAY DIFFRACTION1allA3101
6X-RAY DIFFRACTION1allB1 - 3
7X-RAY DIFFRACTION1allB5 - 6
8X-RAY DIFFRACTION1allS1 - 765
9X-RAY DIFFRACTION1allC1
10X-RAY DIFFRACTION1allD1 - 2
11X-RAY DIFFRACTION1allE1
12X-RAY DIFFRACTION1allF1

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