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- PDB-1th7: Crystal Structure of an Archaeal Sm Protein from Sulfolobus solfa... -

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Basic information

Entry
Database: PDB / ID: 1th7
TitleCrystal Structure of an Archaeal Sm Protein from Sulfolobus solfataricus
ComponentsSmall nuclear riboprotein protein
KeywordsRNA BINDING PROTEIN / archaea / SM protein / SM fold / SS-SM1
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
Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKilic, T. / Suck, D.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of an archaeal Sm protein from Sulfolobus solfataricus
Authors: Kilic, T. / Thore, S. / Suck, D.
History
DepositionJun 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small nuclear riboprotein protein
B: Small nuclear riboprotein protein
C: Small nuclear riboprotein protein
D: Small nuclear riboprotein protein
E: Small nuclear riboprotein protein
F: Small nuclear riboprotein protein
G: Small nuclear riboprotein protein
H: Small nuclear riboprotein protein
I: Small nuclear riboprotein protein
J: Small nuclear riboprotein protein
K: Small nuclear riboprotein protein
L: Small nuclear riboprotein protein
M: Small nuclear riboprotein protein
N: Small nuclear riboprotein protein


Theoretical massNumber of molelcules
Total (without water)123,45414
Polymers123,45414
Non-polymers00
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30710 Å2
ΔGint-154 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.180, 66.810, 129.010
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Small nuclear riboprotein protein / snRNP-2


Mass: 8818.146 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: snRNP-2 / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97ZQ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 48.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG 3350, 0.3M Lithium Sulfate, 0.1M Tris Buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. all: 133678 / Num. obs: 132245 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.7 Å2
Reflection shellResolution: 1.68→1.74 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I4K

1i4k


Resolution: 1.68→35.28 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2411083.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 6658 5 %RANDOM
Rwork0.217 ---
all0.228 132219 --
obs0.228 132219 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9717 Å2 / ksol: 0.374549 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å2-2.6 Å2
2---2.18 Å20 Å2
3----0.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.68→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8302 0 0 474 8776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 1.68→1.74 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 1058 4.9 %
Rwork0.242 20547 -
obs-20547 97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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