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- PDB-6fa9: CRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 -

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Basic information

Entry
Database: PDB / ID: 6fa9
TitleCRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2
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 / Helicase associated domain (HA2), winged-helix ...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 / Helicase associated domain (HA2), winged-helix / 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSchmitt, A. / Hamann, F. / 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 / 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: Putative mRNA splicing factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1133
Polymers72,9211
Non-polymers1922
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-34 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 114.130, 120.690
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: 72920.586 Da / Num. of mol.: 1 / Fragment: residues 3-610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063660 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SEG4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/HCl pH 7.5, 0.20 M Li2SO4, 15% (w/v) PEG 8000
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 7, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→41.462 Å / Num. obs: 22177 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.861 % / Biso Wilson estimate: 50.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.078 / Χ2: 0.975 / Net I/σ(I): 20.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.74.9830.842.3423040.8250.93699.9
2.7-2.84.9260.5773.3120420.9010.64399.9
2.8-34.9450.3715.132630.9540.41399.9
3-3.664.9150.12712.7664350.9940.142100
3.66-3.994.8980.05227.0318040.9980.05999.8
3.99-4.324.8210.03734.9313180.9990.04299.8
4.32-4.654.8140.03339.579690.9990.03799.9
4.65-144.6430.02250.57387710.02599.5
14-174.2760.01384.227610.01598.7
17-503.5390.01474.36890.9990.01690.8
41.462-50

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAA

6faa


Resolution: 2.6→41.462 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.49
RfactorNum. reflection% reflection
Rfree0.2759 1109 5 %
Rwork0.23 --
obs0.2323 22168 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 195.17 Å2 / Biso mean: 69.9971 Å2 / Biso min: 23.06 Å2
Refinement stepCycle: final / Resolution: 2.6→41.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 10 42 5020
Biso mean--77.14 45.22 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045072
X-RAY DIFFRACTIONf_angle_d0.8526884
X-RAY DIFFRACTIONf_chiral_restr0.062789
X-RAY DIFFRACTIONf_plane_restr0.009892
X-RAY DIFFRACTIONf_dihedral_angle_d12.0393104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.71850.33991370.328925862723100
2.7185-2.86180.33831360.315125802716100
2.8618-3.0410.34161370.295526072744100
3.041-3.27570.31261370.281325902727100
3.2757-3.60520.27971380.254526322770100
3.6052-4.12650.25551380.21226232761100
4.1265-5.19730.23391400.19226572797100
5.1973-41.46740.26541460.19142784293099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.29821.1296-0.0664.41140.14181.2283-0.0221-0.0388-0.185-0.2550.0487-0.43910.04630.2051-0.01820.19150.05120.05140.3637-0.00940.3026-11.448410.993-40.7694
20.17920.3547-0.08855.08161.41261.0006-0.1197-0.0790.05330.40590.01520.34260.0553-0.01250.05640.32130.0603-0.00170.37930.03010.3605-21.911622.5403-29.3127
31.58710.23151.39564.268-0.08433.0239-0.115-0.3928-0.09021.58460.23650.35070.4411-0.1521-0.10091.27560.25640.09360.71720.0870.5176-17.604312.0836-8.6832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 283 through 615 )A283 - 615
2X-RAY DIFFRACTION2chain 'A' and (resid 616 through 736 )A616 - 736
3X-RAY DIFFRACTION3chain 'A' and (resid 737 through 921 )A737 - 921

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