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- PDB-5r09: PanDDA analysis group deposition -- Aar2/RNaseH in complex with f... -

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Basic information

Entry
Database: PDB / ID: 5r09
TitlePanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry B03, DMSO-free
Components
  • A1 cistron-splicing factor AAR2
  • Pre-mRNA-splicing factor 8
KeywordsSPLICING / FragMAX / FragMAXapp / fragment screening / RNaseH like domain / VHS like domain / U5 snRNP assembly
Function / homology
Function and homology information


generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain ...Aar2, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / A1 cistron-splicing factor, AAR2 / AAR2, N-terminal / AAR2, C-terminal / AAR2, C-terminal domain superfamily / AAR2, N-terminal domain superfamily / AAR2 C-terminal repeat region / AAR2 N-terminal domain / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Ribonuclease H-like superfamily / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-[(1~{S})-1-azanylpropyl]phenol / A1 cistron-splicing factor AAR2 / Pre-mRNA-splicing factor 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsWollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
CitationJournal: Structure / Year: 2020
Title: F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.
Authors: Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 10, 2021Group: Data collection
Category: diffrn_detector / diffrn_radiation / diffrn_source
Item: _diffrn_detector.pdbx_collection_date / _diffrn_detector.type ..._diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Pre-mRNA-splicing factor 8
B: A1 cistron-splicing factor AAR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8623
Polymers65,7112
Non-polymers1511
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.612, 81.915, 93.845
Angle α, β, γ (deg.)90.000, 108.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pre-mRNA-splicing factor 8


Mass: 29501.113 Da / Num. of mol.: 1 / Fragment: yPrp8 RNaseH (UNP Residues 1836-2096)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334
#2: Protein A1 cistron-splicing factor AAR2


Mass: 36209.836 Da / Num. of mol.: 1 / Fragment: GAMA - Aar2(1-152) - SSSSS - Aar2(171-317) / Mutation: L153_D170delinsSSSSS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357
#3: Chemical ChemComp-SYG / 2-[(1~{S})-1-azanylpropyl]phenol


Mass: 151.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H13NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 49.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 4000, 0.2M Tris-HCl pH 8.5, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.827 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.56→22.07 Å / Num. obs: 90548 / % possible obs: 99.6 % / Redundancy: 6.867 % / Biso Wilson estimate: 36.109 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Χ2: 1.028 / Net I/σ(I): 17.32 / Num. measured all: 622668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsCC1/2Rrim(I) allRejects% possible all
1.56-1.656.762.3550.769884214625143540.392.548670.981
1.65-1.777.051.331.419736713814137970.6651.43640.999
1.77-1.916.970.6412.938945012838128240.8920.693420.999
1.91-2.096.590.2716.567792211826118100.9750.295400.999
2.09-2.336.590.12413.577049210691106840.9940.13510.999
2.33-2.697.20.06925.4268113945594520.9980.07401
2.69-3.36.920.03743.5355462800980040.9990.0410.999
3.3-4.656.250.02265.8639155626062440.9990.02410.997
4.65-507.370.02279.9825865350934970.9990.02400.997

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.56→22.07 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 2100 2.32 %
Rwork0.2034 88449 -
obs0.2043 90548 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.33 Å2 / Biso mean: 46.4975 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.56→22.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 27 172 4601
Biso mean--51.82 40.26 -
Num. residues----537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.590.45151340.44235654578895
1.59-1.630.43451390.400158405979100
1.63-1.680.38211410.357859316072100
1.68-1.730.33871390.320458535992100
1.73-1.780.37081400.299159136053100
1.78-1.850.37081390.273258435982100
1.85-1.920.28531410.251459256066100
1.92-2.010.26031400.23459206060100
2.01-2.110.28031390.222158746013100
2.11-2.240.2391410.213759316072100
2.24-2.420.25891400.204159286068100
2.42-2.660.27551410.213959076048100
2.66-3.050.23891410.216359486089100
3.05-3.830.23891410.191259436084100
3.83-22.070.18111430.155360396182100

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