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- PDB-6tfl: Lsm protein (SmAP) from Halobacterium salinarum -

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Basic information

Entry
Database: PDB / ID: 6tfl
TitleLsm protein (SmAP) from Halobacterium salinarum
ComponentsRNA-binding protein Lsm
KeywordsRNA BINDING PROTEIN / Lsm / SmAP / RNA-chaperon
Function / homologyLSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / LSM domain superfamily / URIDINE / RNA-binding protein Lsm
Function and homology information
Biological speciesHalobacterium salinarum R1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å
AuthorsNikulin, A.D. / Fando, M.S. / Lekontseva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00222 Russian Federation
CitationJournal: Biochemistry Mosc. / Year: 2021
Title: Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum.
Authors: Fando, M.S. / Mikhaylina, A.O. / Lekontseva, N.V. / Tishchenko, S.V. / Nikulin, A.D.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein Lsm
B: RNA-binding protein Lsm
C: RNA-binding protein Lsm
D: RNA-binding protein Lsm
E: RNA-binding protein Lsm
F: RNA-binding protein Lsm
G: RNA-binding protein Lsm
H: RNA-binding protein Lsm
I: RNA-binding protein Lsm
J: RNA-binding protein Lsm
K: RNA-binding protein Lsm
L: RNA-binding protein Lsm
M: RNA-binding protein Lsm
N: RNA-binding protein Lsm
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,37857
Polymers94,74514
Non-polymers4,63343
Water5,567309
1
A: RNA-binding protein Lsm
B: RNA-binding protein Lsm
C: RNA-binding protein Lsm
D: RNA-binding protein Lsm
E: RNA-binding protein Lsm
F: RNA-binding protein Lsm
G: RNA-binding protein Lsm
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,61526
Polymers47,3737
Non-polymers2,24219
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15850 Å2
ΔGint-62 kcal/mol
Surface area17350 Å2
MethodPISA
2
H: RNA-binding protein Lsm
I: RNA-binding protein Lsm
J: RNA-binding protein Lsm
K: RNA-binding protein Lsm
L: RNA-binding protein Lsm
M: RNA-binding protein Lsm
N: RNA-binding protein Lsm
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,76331
Polymers47,3737
Non-polymers2,39124
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16040 Å2
ΔGint-85 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.450, 156.450, 106.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
RNA-binding protein Lsm


Mass: 6767.518 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: This protein has two additional amino acid residues at the N-terminus because of TEV protease specificity.
Source: (gene. exp.) Halobacterium salinarum R1 (Halophile) / Gene: lsm, snp, OE_3142R / Production host: Escherichia coli (E. coli) / References: UniProt: B0R5R2
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-URI / URIDINE / Uridine


Mass: 244.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 8000; 100mM MES pH=6.5; 200mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.397→50 Å / Num. obs: 1318697 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.069 / Rrim(I) all: 0.061 / Χ2: 1.36 / Net I/σ(I): 14
Reflection shellResolution: 2.397→2.483 Å / Redundancy: 15 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 82803 / CC1/2: 0.891 / Rpim(I) all: 0.232 / Rrim(I) all: 0.937 / Χ2: 1.11 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LJO

1ljo


Resolution: 2.397→50 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2306 2700 5.17 %
Rwork0.1777 --
obs0.1805 52247 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.34 Å2 / Biso mean: 47.4693 Å2 / Biso min: 26 Å2
Refinement stepCycle: final / Resolution: 2.397→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 0 310 6904
Biso mean---49.13 -
Num. residues----911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3971-2.44070.33961530.2843248697
2.4407-2.48760.36181450.25532564100
2.4876-2.53840.25351290.24482576100
2.5384-2.59360.30041440.24122569100
2.5936-2.65390.281260.23282578100
2.6539-2.72030.30541480.21952566100
2.7203-2.79380.27651270.22482610100
2.7938-2.8760.25831340.21152589100
2.876-2.96880.29831470.20012573100
2.9688-3.07490.29861420.20512597100
3.0749-3.1980.26151490.19932580100
3.198-3.34350.2221340.19062609100
3.3435-3.51980.25261320.16952611100
3.5198-3.74020.19781450.14942607100
3.7402-4.02890.19211630.14892620100
4.0289-4.43410.15771540.12462618100
4.4341-5.07510.16681140.12372692100
5.0751-6.3920.21391470.18142681100
6.392-500.24351670.18832821100

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