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- PDB-5r1d: PanDDA analysis group deposition -- Auto-refined data of Aar2/RNa... -

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Basic information

Entry
Database: PDB / ID: 5r1d
TitlePanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 28, 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: 1.82 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
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.052, 82.645, 92.874
Angle α, β, γ (deg.)90.000, 107.980, 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.: 113 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
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: 1.82→22.66 Å / Num. obs: 57388 / % possible obs: 99.7 % / Redundancy: 6.826 % / Biso Wilson estimate: 50.917 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.046 / Χ2: 1.049 / Net I/σ(I): 20.34 / Num. measured all: 392217
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
1.82-1.936.812.1610.863117927091500.4232.338530.987
1.93-2.066.680.9241.9158216871987100.7941.00310.999
2.06-2.236.190.3974.2150310812681160.9340.43400.999
2.23-2.447.250.1969.2854356749674860.9870.21100.999
2.44-2.727.230.09818.0448746674367450.9960.10521
2.72-3.1470.0533.141948599259880.9990.05450.999
3.14-3.856.40.02953.2232528508650750.9990.03200.998
3.85-5.426.740.02270.5326661395739520.9990.02400.999
5.42-507.260.02577.0816335224922340.9990.02700.993

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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: 1.82→22.66 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 2094 3.65 %
Rwork0.2165 55291 -
obs0.2185 57388 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 297.71 Å2 / Biso mean: 79.4138 Å2 / Biso min: 32.42 Å2
Refinement stepCycle: final / Resolution: 1.82→22.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 16 113 4531
Biso mean--103.12 66.58 -
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 (%)
1.82-1.860.47571350.46563566370197
1.86-1.910.39651390.39936883827100
1.91-1.960.36021400.345936653805100
1.96-2.020.37171400.307737053845100
2.02-2.080.35081380.294936293767100
2.08-2.160.30041400.265136743814100
2.16-2.240.34711400.251236953835100
2.24-2.340.29821400.248637233863100
2.34-2.470.31771380.254736433781100
2.47-2.620.34051400.259936803820100
2.62-2.820.30861410.265137163857100
2.82-3.110.31881400.266236903830100
3.11-3.560.27821410.237937293870100
3.56-4.470.24311410.174737073848100
4.47-22.660.20581440.15837813925100
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)
12.0319-0.2984-0.2940.01880.24161.19030.0443-0.0224-0.1125-0.1923-0.0472-0.0801-0.0206-0.043200.50070.00380.01850.40710.10850.440138.22068.209325.7942
22.0445-0.54720.78521.4625-0.44470.8981-0.05520.3037-0.1481-0.2917-0.0320.05110.1888-0.138900.4538-0.01060.01950.41660.06350.283528.275812.169120.8828
31.7029-0.94210.51151.27360.14281.6911-0.0547-0.20530.3009-0.03950.0828-0.1985-0.04560.1186-0.00010.3579-0.00960.0220.4180.08160.464243.137116.916235.4586
41.19570.19230.46880.26560.23851.10760.0334-0.18650.3826-0.12450.0292-0.3235-0.1640.4430.00010.513-0.06590.04130.5356-0.01080.686651.669824.968736.5146
50.1367-0.20560.32370.2968-0.11610.56-0.07410.07160.0208-0.1909-0.10250.08660.0578-0.218600.5625-0.0223-0.05410.47-0.12570.53311.973911.8302-29.6482
60.8440.2690.05221.2685-0.14452.95610.00630.0023-0.0403-0.359-0.11250.36920.1329-0.4534-0.0010.3542-0.0367-0.0840.4803-0.16960.52786.51587.5029-27.7055
70.21360.2513-0.01920.53640.80261.7584-0.078-0.22050.17090.0387-0.12920.0875-0.0446-0.52540.00010.456-0.0242-0.00420.5586-0.12280.435417.17434.7048-2.6296
81.0429-0.2210.71220.80930.95231.3237-0.0279-0.09120.0427-0.2164-0.0461-0.09570.33610.2223-0.00010.5016-0.02840.00920.4874-0.0710.510531.1636-0.6883-10.9049
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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