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- PDB-5mkl: Crystal structure of SmAP (LSm) protein from Sulfolobus acidocaldarius -

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Basic information

Entry
Database: PDB / ID: 5mkl
TitleCrystal structure of SmAP (LSm) protein from Sulfolobus acidocaldarius
ComponentsSm ribonucleo
KeywordsRNA BINDING PROTEIN / Lsm / SmAP / RNA-binding protein
Function / homologySm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / LSM domain superfamily / mRNA splicing, via spliceosome / Sm ribonucleo
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.086 Å
AuthorsNikulin, A.D. / Lekontseva, N.V. / Tishchenko, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Scientific Foundation14-14-00496 Russian Federation
CitationJournal: Biochimie / Year: 2020
Title: Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.
Authors: Lekontseva, N. / Mikhailina, A. / Fando, M. / Kravchenko, O. / Balobanov, V. / Tishchenko, S. / Nikulin, A.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible
Revision 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A1: Sm ribonucleo
B1: Sm ribonucleo
C1: Sm ribonucleo
D1: Sm ribonucleo
E1: Sm ribonucleo
F1: Sm ribonucleo
G1: Sm ribonucleo
A2: Sm ribonucleo
B2: Sm ribonucleo
C2: Sm ribonucleo
D2: Sm ribonucleo
E2: Sm ribonucleo
F2: Sm ribonucleo
G2: Sm ribonucleo
A3: Sm ribonucleo
B3: Sm ribonucleo
C3: Sm ribonucleo
D3: Sm ribonucleo
E3: Sm ribonucleo
F3: Sm ribonucleo
G3: Sm ribonucleo
A4: Sm ribonucleo
B4: Sm ribonucleo
C4: Sm ribonucleo
D4: Sm ribonucleo
E4: Sm ribonucleo
F4: Sm ribonucleo
G4: Sm ribonucleo


Theoretical massNumber of molelcules
Total (without water)274,60728
Polymers274,60728
Non-polymers00
Water8,233457
1
A1: Sm ribonucleo
B1: Sm ribonucleo
C1: Sm ribonucleo
D1: Sm ribonucleo
E1: Sm ribonucleo
F1: Sm ribonucleo
G1: Sm ribonucleo


Theoretical massNumber of molelcules
Total (without water)68,6527
Polymers68,6527
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-67 kcal/mol
Surface area23490 Å2
MethodPISA
2
A2: Sm ribonucleo
B2: Sm ribonucleo
C2: Sm ribonucleo
D2: Sm ribonucleo
E2: Sm ribonucleo
F2: Sm ribonucleo
G2: Sm ribonucleo


Theoretical massNumber of molelcules
Total (without water)68,6527
Polymers68,6527
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-63 kcal/mol
Surface area22750 Å2
MethodPISA
3
A3: Sm ribonucleo
B3: Sm ribonucleo
C3: Sm ribonucleo
D3: Sm ribonucleo
E3: Sm ribonucleo
F3: Sm ribonucleo
G3: Sm ribonucleo


Theoretical massNumber of molelcules
Total (without water)68,6527
Polymers68,6527
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-67 kcal/mol
Surface area23230 Å2
MethodPISA
4
A4: Sm ribonucleo
B4: Sm ribonucleo
C4: Sm ribonucleo
D4: Sm ribonucleo
E4: Sm ribonucleo
F4: Sm ribonucleo
G4: Sm ribonucleo


Theoretical massNumber of molelcules
Total (without water)68,6527
Polymers68,6527
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-65 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.622, 133.516, 135.774
Angle α, β, γ (deg.)86.18, 85.78, 89.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
Sm ribonucleo


Mass: 9807.395 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: ATY89_02410, ATZ20_05445 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0U3FHU0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 8% Tacsimate pH 4.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.085→50 Å / Num. obs: 148188 / % possible obs: 94.7 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.9
Reflection shellResolution: 2.085→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.444 / % possible all: 70.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XQ3

4xq3


Resolution: 2.086→45.034 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.4
RfactorNum. reflection% reflection
Rfree0.2334 7051 5.03 %
Rwork0.1816 --
obs0.1841 140302 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.086→45.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17535 0 0 457 17992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717703
X-RAY DIFFRACTIONf_angle_d0.87523777
X-RAY DIFFRACTIONf_dihedral_angle_d3.62611041
X-RAY DIFFRACTIONf_chiral_restr0.0562813
X-RAY DIFFRACTIONf_plane_restr0.0052981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.086-2.10940.37761450.34312671X-RAY DIFFRACTION58
2.1094-2.13430.36562260.30114421X-RAY DIFFRACTION95
2.1343-2.16030.30672730.26764478X-RAY DIFFRACTION96
2.1603-2.18760.30712490.25674431X-RAY DIFFRACTION94
2.1876-2.21640.28312660.24164403X-RAY DIFFRACTION94
2.2164-2.24680.30282710.23094307X-RAY DIFFRACTION93
2.2468-2.27890.27912370.22154138X-RAY DIFFRACTION90
2.2789-2.31290.29232980.22614531X-RAY DIFFRACTION97
2.3129-2.3490.29332430.21634603X-RAY DIFFRACTION97
2.349-2.38750.29822170.2234625X-RAY DIFFRACTION97
2.3875-2.42870.26822300.20884469X-RAY DIFFRACTION97
2.4287-2.47290.2662320.20194535X-RAY DIFFRACTION96
2.4729-2.52040.27832450.19594682X-RAY DIFFRACTION97
2.5204-2.57190.23812270.19714462X-RAY DIFFRACTION96
2.5719-2.62780.2792220.20134455X-RAY DIFFRACTION96
2.6278-2.68890.23032160.18644500X-RAY DIFFRACTION95
2.6889-2.75610.26612340.19544483X-RAY DIFFRACTION93
2.7561-2.83060.2792200.19554363X-RAY DIFFRACTION95
2.8306-2.91390.23642220.1814655X-RAY DIFFRACTION98
2.9139-3.00790.26022280.18814624X-RAY DIFFRACTION97
3.0079-3.11540.23472540.18224492X-RAY DIFFRACTION98
3.1154-3.24010.23612760.18654642X-RAY DIFFRACTION97
3.2401-3.38760.24532320.17524420X-RAY DIFFRACTION96
3.3876-3.56610.22572380.17214576X-RAY DIFFRACTION95
3.5661-3.78940.22642200.17154412X-RAY DIFFRACTION96
3.7894-4.08180.2122010.17544695X-RAY DIFFRACTION98
4.0818-4.49220.19661920.14414655X-RAY DIFFRACTION98
4.4922-5.14150.16952800.13474468X-RAY DIFFRACTION96
5.1415-6.47460.2392070.19674484X-RAY DIFFRACTION96
6.4746-450.20522500.16964571X-RAY DIFFRACTION97

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