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

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Basic information

Entry
Database: PDB / ID: 6faa
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 / ETHANOL / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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

Downloads & links

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Assembly

Deposited unit
A: Putative mRNA splicing factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7878
Polymers72,9211
Non-polymers8667
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-15 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.260, 114.210, 117.840
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 Putative mRNA splicing factor


Mass: 72920.586 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 270-921
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: pASG-IBA25 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SEG4

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Non-polymers , 5 types, 452 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20 M NaCl, 15% (w/v) PEG8000, 0.1 M Tris/HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9202 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 48358 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 24.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.107 / Χ2: 0.946 / Net I/σ(I): 13.43
Reflection shellResolution: 1.97→2.07 Å / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.77 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XAU

2xau


Resolution: 1.97→46.003 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.17
RfactorNum. reflection% reflection
Rfree0.2242 2420 5.01 %
Rwork0.1875 --
obs0.1894 48349 99.02 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.97 Å2 / Biso mean: 29.8313 Å2 / Biso min: 9.69 Å2
Refinement stepCycle: final / Resolution: 1.97→46.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 58 445 5480
Biso mean--33.18 34.72 -
Num. residues----637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055207
X-RAY DIFFRACTIONf_angle_d1.0517073
X-RAY DIFFRACTIONf_chiral_restr0.053807
X-RAY DIFFRACTIONf_plane_restr0.01915
X-RAY DIFFRACTIONf_dihedral_angle_d27.325447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9701-2.01030.32821430.29832696283999
2.0103-2.0540.31461380.27182631276999
2.054-2.10180.28791430.24972695283899
2.1018-2.15430.30261400.236526542794100
2.1543-2.21260.26221410.228426902831100
2.2126-2.27770.26071440.21462718286299
2.2777-2.35120.25161390.207526422781100
2.3512-2.43520.27071410.20312693283499
2.4352-2.53270.24111430.201927082851100
2.5327-2.6480.24511420.203627092851100
2.648-2.78760.24881430.19942711285499
2.7876-2.96220.24661420.19752685282799
2.9622-3.19090.23661420.19272711285399
3.1909-3.51190.21021440.17732722286699
3.5119-4.01980.19251420.15412716285898
4.0198-5.06350.17171450.13272741288698
5.0635-46.01510.1641480.16842807295596
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)
11.10610.01720.3350.43240.2370.98310.14940.274-0.098-0.29210.0184-0.0971-0.02770.05070.15090.20320.02210.0380.2275-0.02760.1739-3.708514.5909-53.9615
20.6395-0.23210.15781.02680.51390.79840.0374-0.04580.08-0.03560.0816-0.1049-0.13460.09560.00290.1429-0.01140.03620.16270.01010.1769-4.737423.1516-39.6936
30.86140.07380.13330.44970.36820.3558-0.05480.16010.0241-0.2414-0.00860.2338-0.0014-0.0971-00.21960.0369-0.02550.2422-0.00290.209-23.807412.1767-48.5205
40.53560.42380.30040.9634-0.05990.54740.0242-0.1109-0.21160.0845-0.0585-0.25020.12280.0749-0.00370.15810.00730.03430.14380.02740.2401-15.2829-4.9347-32.877
50.65590.23810.01530.4586-0.25990.2084-0.00980.06020.0697-0.056-0.06990.1312-0.1026-0.0955-0.00020.16560.0085-0.00390.1801-0.01280.2316-27.289310.0463-35.7602
60.2511-0.0979-0.07370.45820.06980.37810.0111-0.02690.01910.0439-0.01810.0826-0.1048-0.05400.17960.03640.01610.1722-0.0150.1916-23.202526.0398-29.1461
70.67050.37820.04141.29230.11240.7635-0.0271-0.1598-0.090.32290.0927-0.13330.14120.07810.00320.29280.0521-0.02630.25650.00440.1808-11.060311.6435-9.2102
80.44930.09580.01390.4820.18090.4871-0.0545-0.1958-0.02170.2684-0.04580.33250.0615-0.3770.00010.31330.00220.0770.3496-0.00770.2897-29.628316.3071-8.3297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 283 through 336 )A283 - 336
2X-RAY DIFFRACTION2chain 'A' and (resid 337 through 450 )A337 - 450
3X-RAY DIFFRACTION3chain 'A' and (resid 451 through 488 )A451 - 488
4X-RAY DIFFRACTION4chain 'A' and (resid 489 through 589 )A489 - 589
5X-RAY DIFFRACTION5chain 'A' and (resid 590 through 631 )A590 - 631
6X-RAY DIFFRACTION6chain 'A' and (resid 632 through 721 )A632 - 721
7X-RAY DIFFRACTION7chain 'A' and (resid 722 through 858 )A722 - 858
8X-RAY DIFFRACTION8chain 'A' and (resid 859 through 921 )A859 - 921

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