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- PDB-5r0q: PanDDA analysis group deposition -- Auto-refined data of Aar2/RNa... -

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Basic information

Entry
Database: PDB / ID: 5r0q
TitlePanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 04, 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
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: 1.91 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


Theoretical massNumber of molelcules
Total (without water)65,7112
Polymers65,7112
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.061, 81.616, 92.250
Angle α, β, γ (deg.)90.000, 108.100, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000

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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: 1.91→23.29 Å / Num. obs: 47659 / % possible obs: 99.3 % / Redundancy: 6.732 % / Biso Wilson estimate: 46.958 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.106 / Χ2: 1.065 / Net I/σ(I): 11.03 / Num. measured all: 321576
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
1.91-2.036.222.3480.7748118773074530.3832.552870.964
2.03-2.176.021.2011.4543729726872600.5881.31760.999
2.17-2.346.980.8012.5647338678467780.850.86630.999
2.34-2.567.180.4374.5944854624562380.950.47140.999
2.56-2.867.130.2268.4840418567056540.9870.244270.997
2.86-3.316.810.11615.2733871497349740.9950.12621
3.31-4.046.080.05727.5625917426042510.9980.06210.998
4.04-5.697.160.03941.5923488328032770.9980.04200.999
5.69-507.290.0446.3413843189918810.9990.04300.991

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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: 1.91→23.29 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 2092 4.39 %
Rwork0.224 45567 -
obs0.2266 47659 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.02 Å2 / Biso mean: 76.6672 Å2 / Biso min: 26.9 Å2
Refinement stepCycle: final / Resolution: 1.91→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 16 60 4478
Biso mean--89.99 66.64 -
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 (%)
1.91-1.960.5041240.47672747287190
1.96-2.010.42931420.413230813223100
2.01-2.060.40791380.379730073145100
2.06-2.120.40861390.358130423181100
2.12-2.190.40591390.312530323171100
2.19-2.270.34031400.282830463186100
2.27-2.360.40221410.272430453186100
2.36-2.460.33541410.26330703211100
2.46-2.590.31931390.252230333172100
2.59-2.760.34851410.26230593200100
2.76-2.970.33161410.259830613202100
2.97-3.270.31551390.260130593198100
3.27-3.740.28411420.220630803222100
3.74-4.70.21331410.164730683209100
4.7-23.290.21731450.164631373282100
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)
11.0156-0.2227-0.20030.39550.68381.21350.05780.0892-0.0323-0.1462-0.14610.0136-0.1228-0.0458-0.00010.41450.00680.03410.34340.08360.384837.74097.899125.6091
21.2918-0.15930.79360.8757-0.07440.4817-0.04070.2222-0.0636-0.295-0.03290.00720.0747-0.0379-0.00020.3674-0.01020.01220.35090.03940.228827.944811.871920.7234
31.1347-0.59350.25540.4188-0.47151.2608-0.0781-0.07390.21790.27790.0392-0.2114-0.01160.1039-00.2703-0.04240.00050.39860.05430.434542.540716.467135.2935
40.6604-0.08210.16980.6395-0.07480.55380.0766-0.34090.06050.2168-0.0705-0.32-0.24090.332-0.0170.2868-0.08640.01020.3956-0.01330.531550.971124.43436.447
50.6761-0.59480.2940.4928-0.20810.5166-0.04110.03070.0449-0.1968-0.08510.18110.171-0.08410.00010.5684-0.0316-0.07180.4587-0.11610.546111.93111.5531-29.4589
61.00860.42150.1340.8089-0.36561.79510.0749-0.0259-0.0387-0.4434-0.06640.39240.1974-0.33490.00030.3972-0.0536-0.07450.4621-0.10090.43896.49197.2751-27.5654
70.01120.07690.1710.11980.45491.753-0.1156-0.23610.07720.1516-0.0740.0325-0.0666-0.37630.00020.4407-0.0156-0.00780.5004-0.09260.395417.03084.5066-2.6835
80.5040.10310.63650.29270.39681.0152-0.135-0.04930.15650.04680.0638-0.12940.26090.1943-00.4751-00.01290.443-0.05440.426730.8635-0.7967-10.8475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1833:1904)A1833 - 1904
2X-RAY DIFFRACTION2(chain A and resid 1905:1964)A1905 - 1964
3X-RAY DIFFRACTION3(chain A and resid 1965:2027)A1965 - 2027
4X-RAY DIFFRACTION4(chain A and resid 2028:2069)A2028 - 2069
5X-RAY DIFFRACTION5(chain B and resid 1:66)B1 - 66
6X-RAY DIFFRACTION6(chain B and resid 67:137)B67 - 137
7X-RAY DIFFRACTION7(chain B and resid 138:251)B138 - 251
8X-RAY DIFFRACTION8(chain B and resid 252:317)B252 - 317

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