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- PDB-3obw: Crystal structure of two archaeal Pelotas reveal inter-domain str... -

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Basic information

Entry
Database: PDB / ID: 3obw
TitleCrystal structure of two archaeal Pelotas reveal inter-domain structural plasticity
ComponentsProtein pelota homolog
KeywordsHYDROLASE / Sm fold
Function / homology
Function and homology information


RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / ribosome binding / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm
Similarity search - Function
Translation release factor pelota, archaea / Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 ...Translation release factor pelota, archaea / Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein pelota homolog
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLee, H.H. / Jang, J.Y. / Yoon, H.-J. / Kim, S.J. / Suh, S.W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structures of two archaeal Pelotas reveal inter-domain structural plasticity
Authors: Lee, H.H. / Jang, J.Y. / Yoon, H.-J. / Kim, S.J. / Suh, S.W.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Protein pelota homolog


Theoretical massNumber of molelcules
Total (without water)41,8581
Polymers41,8581
Non-polymers00
Water1629
1
A: Protein pelota homolog

A: Protein pelota homolog


Theoretical massNumber of molelcules
Total (without water)83,7172
Polymers83,7172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2690 Å2
ΔGint-8 kcal/mol
Surface area31600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.394, 34.329, 90.109
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein pelota homolog


Mass: 41858.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P96026, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM imidazole pH 8.0, 1.0M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONPAL/PLS 4A20.97867, 0.97935, 0.97099
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDMar 1, 2006
ADSC QUANTUM 4r2CCDMar 1, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978671
30.979351
40.970991
ReflectionResolution: 2.6→15 Å / Num. all: 11686 / Num. obs: 10800 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1120 -Random
Rwork0.228 ---
all-11686 --
obs-10800 92.4 %-
Displacement parametersBiso mean: 63.7938 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 0 9 2601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.439
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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