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- PDB-5r19: PanDDA analysis group deposition -- Auto-refined data of Aar2/RNa... -

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Basic information

Entry
Database: PDB / ID: 5r19
TitlePanDDA analysis group deposition -- Auto-refined data of Aar2/RNaseH for ground state model 24, 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 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding ...generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 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 / AAR2 N-terminal domain / 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, C-terminal domain-like / Substrate Binding Domain Of DNAk; Chain A, domain 1 - #20 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / AAR2 N-terminal domain / 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 / 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: 1.7 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

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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
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.083, 82.486, 92.585
Angle α, β, γ (deg.)90.000, 107.760, 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 / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
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: 1.7→23.3 Å / Num. obs: 69377 / % possible obs: 99.7 % / Redundancy: 6.855 % / Biso Wilson estimate: 46.147 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.054 / Χ2: 1.024 / Net I/σ(I): 17.01 / Num. measured all: 476059
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
1.7-1.86.892.9560.537741911235111020.2533.196610.988
1.8-1.936.961.3671.247324510527105220.6181.479101
1.93-2.086.590.5783.0364556980397950.8880.62920.999
2.08-2.286.430.2546.8957970901090060.9730.27701
2.28-2.547.250.12314.7759452820081940.9940.13300.999
2.54-2.947.170.06326.9351891724272340.9980.068130.999
2.94-3.596.680.03644.7340962613461270.9990.03900.999
3.59-5.076.420.02561.3830737478447750.9990.02800.998
5.07-507.330.02869.5619827270626950.9990.0300.996

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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: 1.7→23.3 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 2095 3.02 %
Rwork0.2 67279 -
obs0.2011 69377 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.76 Å2 / Biso mean: 68.4917 Å2 / Biso min: 31.31 Å2
Refinement stepCycle: final / Resolution: 1.7→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 16 128 4546
Biso mean--94.63 50.45 -
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 (%)
1.7-1.740.41771360.42664360449697
1.74-1.780.46151400.424144914631100
1.78-1.830.41861390.428144704609100
1.83-1.880.39181400.355844564596100
1.88-1.940.31491390.304244684607100
1.94-2.010.27551410.266545084649100
2.01-2.090.29231390.251844564595100
2.09-2.190.27791390.23744564595100
2.19-2.30.23511400.217345124652100
2.3-2.450.26741400.215244744614100
2.45-2.640.24341400.218845134653100
2.64-2.90.25751400.223544904630100
2.9-3.320.27261400.224845084648100
3.32-4.180.21781410.169645284669100
4.18-23.30.19191440.152445894733100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5938-0.4054-0.29180.42010.45361.10550.08240.0279-0.1909-0.2707-0.08270.0395-0.0547-0.080700.42870.00970.0190.3580.08510.411837.84677.905825.6968
21.3772-0.13620.64251.0949-0.09590.8644-0.03530.2927-0.1245-0.2973-0.06730.04680.1114-0.1467-00.44970.01510.00790.44790.05570.343927.890111.889720.8712
31.0114-0.29670.13190.86360.46711.8046-0.0166-0.23950.208-0.02640.0649-0.1966-0.0890.1675-0.00010.3358-0.00750.01720.40320.0660.420942.813916.621535.3111
40.641-0.30650.16910.20080.11910.83250.1795-0.2250.2784-0.1029-0.0452-0.2445-0.17680.4719-0.00030.4332-0.05850.04820.5242-0.02170.572351.325824.670636.3423
50.25550.01630.17410.23870.18960.7253-0.03090.15270.0632-0.3067-0.01450.20130.1281-0.15310.00010.5267-0.0079-0.05280.452-0.10190.518611.75211.5791-29.5687
60.85780.699-0.07561.0222-0.50012.2259-0.0265-0.03790.0453-0.3044-0.03580.33920.2229-0.4857-0.00020.4511-0.0396-0.08480.5065-0.1410.53176.28517.2752-27.6677
7-0.1412-0.03860.04320.73530.01871.8318-0.1164-0.16540.14120.0648-0.08120.0829-0.0648-0.39830.00020.441-0.0359-0.00070.5268-0.10720.421116.7944.4465-2.5633
81.13960.04750.44670.84691.32021.4631-0.0386-0.01090.116-0.08310.1086-0.0930.22860.1683-0.00020.4644-0.01320.01660.4491-0.04880.454730.7772-0.9791-10.7514
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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