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- PDB-1tlj: Crystal Structure of Conserved Protein of Unknown Function SSO062... -

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Basic information

Entry
Database: PDB / ID: 1tlj
TitleCrystal Structure of Conserved Protein of Unknown Function SSO0622 from Sulfolobus solfataricus
ComponentsHypothetical UPF0130 protein SSO0622
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Midwest Center for Structural Genomics / SSO0622 / PSI / Protein Structure Initiative / MCSG
Function / homology
Function and homology information


tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase / tRNA methyltransferase activity / wybutosine biosynthetic process / tRNA methylation / cytoplasm
Similarity search - Function
SSo0622-like fold / tRNA wybutosine-synthesizing-like / tRNA wybutosine-synthesizing protein / tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase / tRNA wybutosine-synthesizing-like superfamily / Methyltransferase TYW3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA(Phe) 7-((3-amino-3-carboxypropyl)-4-demethylwyosine(37)-N(4))-methyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsJia, Z. / Wong, A.H.Y. / Kudrytska, M. / Skarina, T. / Walker, J. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Rna / Year: 2017
Title: Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases.
Authors: Currie, M.A. / Brown, G. / Wong, A. / Ohira, T. / Sugiyama, K. / Suzuki, T. / Yakunin, A.F. / Jia, Z.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0130 protein SSO0622
B: Hypothetical UPF0130 protein SSO0622
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2735
Polymers48,9852
Non-polymers2883
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-65 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.114, 92.114, 110.907
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Hypothetical UPF0130 protein SSO0622


Mass: 24492.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0622, C08_028
Plasmid details: pED15b thrombin site modified to TEV cleavage site
Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UX16
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.8 Å3/Da / Density % sol: 0.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 5000MME, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927,0.97948, 0.96404
DetectorType: SBC-3 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979481
30.964041
ReflectionResolution: 2.8→50 Å / Num. all: 25954 / Num. obs: 25954 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.082 / Rsym value: 0.078 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.99 / Num. unique all: 2600 / Rsym value: 0.358 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / σ(F): 1 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 2392 -Random
Rwork0.2232 ---
all0.2489 25954 --
obs0.2489 25954 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 15 249 3348

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