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- PDB-6fa5: CRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 IN COMPLEX WITH ADP -

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Basic information

Entry
Database: PDB / ID: 6fa5
TitleCRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 IN COMPLEX WITH ADP
ComponentsPutative mRNA splicing factor
KeywordsHYDROLASE / SPLICING / ATPASE / HELICASE / G-PATCH
Function / homology
Function and homology information


catalytic step 2 spliceosome / RNA splicing / helicase activity / mRNA processing / hydrolase activity / RNA helicase / RNA binding / ATP binding / metal ion binding
Similarity search - Function
G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding 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 ...G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding 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 / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / 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 / DI(HYDROXYETHYL)ETHER / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.303 Å
AuthorsHamann, F. / Schmitt, A. / Neumann, P. / Ficner, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of the spliceosomal DEAH-box ATPase Prp2.
Authors: Schmitt, A. / Hamann, F. / Neumann, P. / Ficner, R.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...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 / 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: Putative mRNA splicing factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3934
Polymers70,8351
Non-polymers5583
Water1,06359
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-15 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.206, 116.412, 118.228
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 Putative mRNA splicing factor


Mass: 70835.133 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063660 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SEG4
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 100mM Na-HEPES, 250mM NaCl, 25% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.3→44.638 Å / Num. obs: 30007 / % possible obs: 99.1 % / Redundancy: 4.282 % / Biso Wilson estimate: 49.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.09 / Χ2: 1.077 / Net I/σ(I): 13.78 / Num. measured all: 128483
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.444.3530.8531.9147020.6530.96897.9
2.44-2.614.3890.5942.9844910.8180.67299.8
2.61-2.824.3530.3734.6642320.9230.42199.7
2.82-3.094.4260.28.3138880.9780.22599.7
3.09-3.454.4050.10914.2835490.9920.12399.4
3.45-3.984.2610.05624.8331170.9970.06499.3
3.98-4.863.9130.0432.526570.9980.04698.6
4.86-6.844.070.03633.4921110.9980.04198.6
6.84-44.6383.7860.02442.812600.9990.02898.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.73 Å44.64 Å
Translation6.73 Å44.64 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAA

6faa


Resolution: 2.303→44.638 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.61
RfactorNum. reflection% reflection
Rfree0.2454 1500 5 %
Rwork0.1979 --
obs0.2003 29999 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.3 Å2 / Biso mean: 58.15 Å2 / Biso min: 26.83 Å2
Refinement stepCycle: final / Resolution: 2.303→44.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 35 59 5051
Biso mean--63.45 53.47 -
Num. residues----635
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 (%)
2.3027-2.37710.35451300.31562472260296
2.3771-2.4620.3691360.307125672703100
2.462-2.56060.32611350.286125702705100
2.5606-2.67710.32921340.271625692703100
2.6771-2.81820.32651350.270525672702100
2.8182-2.99480.28161360.231925842720100
2.9948-3.22590.30231370.226825982735100
3.2259-3.55040.27241360.21232577271399
3.5504-4.06390.23491380.16692621275999
4.0639-5.11890.16621370.14942608274598
5.1189-44.64640.20481460.16492766291299

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