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- PDB-2ax5: Solution Structure of Urm1 from Saccharomyces Cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2ax5
TitleSolution Structure of Urm1 from Saccharomyces Cerevisiae
ComponentsHypothetical 11.0 kDa protein in FAA3-MAS3 intergenic region
KeywordsSIGNALING PROTEIN / Beta grasp fold
Function / homology
Function and homology information


cell budding / tRNA thio-modification / sulfur carrier activity / tRNA wobble position uridine thiolation / protein urmylation / invasive growth in response to glucose limitation / tRNA wobble uridine modification / protein tag activity / cellular response to oxidative stress / protein homodimerization activity ...cell budding / tRNA thio-modification / sulfur carrier activity / tRNA wobble position uridine thiolation / protein urmylation / invasive growth in response to glucose limitation / tRNA wobble uridine modification / protein tag activity / cellular response to oxidative stress / protein homodimerization activity / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-related modifier 1 / Urm1 (Ubiquitin related modifier) / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-related modifier 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsXu, J. / Huang, H. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Solution structure of Urm1 and its implications for the origin of protein modifiers.
Authors: Xu, J. / Zhang, J. / Wang, L. / Zhou, J. / Huang, H. / Wu, J. / Zhong, Y. / Shi, Y.
History
DepositionSep 3, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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: Hypothetical 11.0 kDa protein in FAA3-MAS3 intergenic region


Theoretical massNumber of molelcules
Total (without water)12,1111
Polymers12,1111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical 11.0 kDa protein in FAA3-MAS3 intergenic region / Ubiquitin-related modifier-1


Mass: 12110.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YIL008W / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40554

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM [15N, 13C] labeled Urm1 protein, 50mM phosphate buffer (pH6.5), 50mM sodium chloride, 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM [15N, 13C] labeled Urm1 protein, 50mM phosphate buffer (pH6.5), 50mM sodium chloride, 100% D2O100% D2O
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
Sparky3T.D.Goddard and D.G.Knellerdata analysis
CNS1.1A.T.Brungerstructure solution
CSI1David S. Wishartdata analysis
MOLMOL2K.2Koradidata analysis
CNS1.1refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structure is solved using a total of 1655 distance restraints and 79 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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