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- PDB-5r04: PanDDA analysis group deposition -- Auto-refined data of Aar2/RNa... -

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Basic information

Entry
Database: PDB / ID: 5r04
TitlePanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 55
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 / F2X-Entry
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: 1.34 Å
AuthorsWeiss, M.S. / Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G.
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 10, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.077, 82.031, 94.300
Angle α, β, γ (deg.)90.000, 108.980, 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 1835-2096)
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.: 205 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 19% (w/v) Peg 4000, 3% (v/v) DMSO, 0.1M Tris-HCl pH 8.5, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.827 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.34→42.15 Å / Num. obs: 132285 / % possible obs: 96.6 % / Redundancy: 7.072 % / Biso Wilson estimate: 28.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.075 / Χ2: 1.114 / Net I/σ(I): 10.84 / Num. measured all: 985861
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
1.34-1.426.562.2360.4515283823290217020.3342.411320.932
1.42-1.526.821.1821.0714905821860208690.6781.272250.955
1.52-1.646.90.6052.4214063820388196210.9040.652510.962
1.64-1.796.820.3344.8512777018725181250.9640.3690.968
1.79-2.016.80.16210.2911548216983165450.990.175100.974
2.01-2.326.840.09218.710262915008147200.9950.09980.981
2.32-2.837.070.06326.838976312701125440.9970.06820.988
2.83-46.990.04735.2768973986397740.9980.0500.991
4-506.980.04539.4338710554454950.9980.048180.991

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMAC5.8.0238phasing
PHENIX1.16.3549refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.34→42.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.704 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23252 7097 5.1 %RANDOM
Rwork0.23164 ---
obs0.2325 132285 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.35 Å2 / Biso mean: 25.521 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20.06 Å2
2---1.24 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.34→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 0 205 4607
Biso mean---30.61 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134714
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174272
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.6416412
X-RAY DIFFRACTIONr_angle_other_deg1.5231.5739969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62423.413252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8371521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025308
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021003
X-RAY DIFFRACTIONr_mcbond_it2.2582.4892251
X-RAY DIFFRACTIONr_mcbond_other2.2552.4882250
X-RAY DIFFRACTIONr_mcangle_it3.2243.7212844
LS refinement shellResolution: 1.338→1.373 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23252 7097 -
Rwork0.23164 9247 -
all-16344 -
obs--91 %

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