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- PDB-2qi2: Crystal structure of the Thermoplasma acidophilum Pelota protein -

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Basic information

Entry
Database: PDB / ID: 2qi2
TitleCrystal structure of the Thermoplasma acidophilum Pelota protein
ComponentsCell division protein pelota related protein
KeywordsCELL CYCLE / Pelota / Dom34
Function / homology
Function and homology information


RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / nonfunctional rRNA decay / 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/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / 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/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / 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 speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsLee, H.H. / Kim, Y.S. / Kim, K.H. / Heo, I.H. / Kim, S.K. / Kim, O. / Suh, S.W.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural and functional insights into dom34, a key component of no-go mRNA decay
Authors: Lee, H.H. / Kim, Y.S. / Kim, K.H. / Heo, I. / Kim, S.K. / Kim, O. / Kim, H.K. / Yoon, J.Y. / Kim, H.S. / Kim, D.J. / Lee, S.J. / Yoon, H.J. / Kim, S.J. / Lee, B.G. / Song, H.K. / Kim, V.N. / ...Authors: Lee, H.H. / Kim, Y.S. / Kim, K.H. / Heo, I. / Kim, S.K. / Kim, O. / Kim, H.K. / Yoon, J.Y. / Kim, H.S. / Kim, D.J. / Lee, S.J. / Yoon, H.J. / Kim, S.J. / Lee, B.G. / Song, H.K. / Kim, V.N. / Park, C.M. / Suh, S.W.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 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

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Assembly

Deposited unit
A: Cell division protein pelota related protein


Theoretical massNumber of molelcules
Total (without water)39,5261
Polymers39,5261
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.064, 98.064, 150.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cell division protein pelota related protein / pelota


Mass: 39526.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9HJ74
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.5673.05
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2971vapor diffusion, hanging drop7.4100mM tri-sodium citrate (pH5.6), '1.0M mono-ammonium dihydrogen phosphate, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
2972vapor diffusion, hanging drop7.4100mM tri-sodium citrate (pH5.6), '1.0M mono-ammonium dihydrogen phosphate, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.97945, 0.97965, 0.97178
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 19, 2005mirrors
ADSC QUANTUM 3152CCDNov 19, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphitesSINGLE WAVELENGTHMx-ray1
2GraphitesMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979451
30.979651
40.971781
ReflectionResolution: 2.9→15 Å / Num. all: 15309 / Num. obs: 15309 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 0.4 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→3.04 Å / Redundancy: 13 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.4 / Num. unique all: 15309 / Rsym value: 0.465 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→14.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 136076.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1474 9.6 %RANDOM
Rwork0.214 ---
obs0.214 15309 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.6944 Å2 / ksol: 0.30367 e/Å3
Displacement parametersBiso mean: 70.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.43 Å20 Å20 Å2
2--8.43 Å20 Å2
3----16.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 0 17 2512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 194 9.4 %
Rwork0.35 1870 -
obs--76.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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