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- PDB-1i5l: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOB... -

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Basic information

Entry
Database: PDB / ID: 1i5l
TitleCRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA
Components
  • 5'-R(*UP*UP*U)-3'
  • PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
KeywordsRNA BINDING PROTEIN/RNA / SNRNP / SM / CORE SNRNP DOMAIN / RNA BINDING PROTEIN / SINGLE-STRANDED RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


ribonucleoprotein complex / RNA binding
Similarity search - Function
snRNP Sm-like, putative, archaea / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...snRNP Sm-like, putative, archaea / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
URIDINE / RNA / Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsToro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D.
CitationJournal: EMBO J. / Year: 2001
Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.
Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D.
History
DepositionFeb 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_biol / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: 5'-R(*UP*UP*U)-3'
Y: 5'-R(*UP*UP*U)-3'
A: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
B: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
C: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
D: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
E: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
F: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
G: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
H: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
I: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
J: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
K: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
L: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
M: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
N: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,20820
Polymers119,23116
Non-polymers9774
Water1,02757
1
U: 5'-R(*UP*UP*U)-3'
A: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
B: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
C: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
D: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
E: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
F: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
G: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,34811
Polymers59,6168
Non-polymers7333
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: 5'-R(*UP*UP*U)-3'
H: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
I: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
J: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
K: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
L: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
M: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
N: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8609
Polymers59,6168
Non-polymers2441
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.858, 130.438, 70.047
Angle α, β, γ (deg.)90, 115.36, 90
Int Tables number4
Space group name H-MP1211
Details: The 14 monomers are organized in two ring-shaped heptamers.

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Components

#1: RNA chain 5'-R(*UP*UP*U)-3'


Mass: 873.540 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1 / AF-SM1


Mass: 8391.709 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0875 / Plasmid: MODIFIED PET24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29386
#3: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG6000, sodium citrate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2sodium citrate11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
212 %PEG60001reservoir
3100 mMsodium citrate1reservoirpH4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. all: 28746 / Num. obs: 28746 / % possible obs: 97.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 82.323 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / Num. unique all: 4203 / Rsym value: 0.354 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 70211 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I4K

1i4k


Resolution: 2.75→25 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1469 -random
Rwork0.225 ---
all0.229 28722 --
obs0.229 28722 97.5 %-
Displacement parametersBiso mean: 82.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å219.2 Å2
2---17.03 Å20 Å2
3---9.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7797 114 68 57 8036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.458 242 -
Rwork0.392 --
obs--97.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.225 / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 82.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor Rfree: 0.458 / Rfactor Rwork: 0.392

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