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- PDB-1m94: Solution Structure of the Yeast Ubiquitin-Like Modifier Protein Hub1 -

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Basic information

Entry
Database: PDB / ID: 1m94
TitleSolution Structure of the Yeast Ubiquitin-Like Modifier Protein Hub1
ComponentsProtein YNR032c-a
KeywordsSTRUCTURAL GENOMICS / SIGNALING PROTEIN / ubiquitin-like fold or beta-grasp fold / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / post-translational protein modification / positive regulation of RNA splicing / mRNA splicing, via spliceosome / protein modification process / protein tag activity / nucleus / cytoplasm
Similarity search - Function
Ubiquitin-like modifier Hub1/Ubl5 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like modifier HUB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Yee, A.A. / Semesi, A. / Edwards, A.M. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2003
Title: Solution Structure of the Yeast Ubiquitin-Like Modifier Protein Hub1
Authors: Ramelot, T.A. / Cort, J.R. / Yee, A.A. / Semesi, A. / Edwards, A.M. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein YNR032c-a


Theoretical massNumber of molelcules
Total (without water)10,4551
Polymers10,4551
Non-polymers00
Water00
1


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

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Components

#1: Protein Protein YNR032c-a / Hub1


Mass: 10454.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YNR032c-a/HUB1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(Gold lamdaDE3) / References: UniProt: Q6Q546

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1313D 13C-separated NOESY
1424D 13C/15N-separated NOESY
NMR detailsText: 1H-13C HSQC on 10% C13, U-15N sample for stereospecific assignments of Leu and Val

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Sample preparation

Details
Solution-IDContentsSolvent system
11-3 mM Hub1, U-15N, 13C, NaOAc, pH 5.090% H2O, 10% D20
21-3 mM Hub1, U-15N, 13C, NaOAc, pH* 4.699% H2O, 1% D20
31-3 mM Hub1, U-15N, NaOAc, pH 5.090% H2O, 10% D20
41-3 mM Hub1, U-15N, 10%-13C, NaOAc, pH 5.090% H2O, 10% D20
Sample conditionsIonic strength: 10 mM NaOAc, 300 mM NaCl / pH: 5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.84Brunger, A.T.structure solution
Felix98MSIprocessing
VNMR6.1CVariancollection
Sparky3.98Goddard, Knellerdata analysis
X-PLOR3.84Brunger, A.T.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 869 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 783; INTRA-RESIDUE [I=J] = 4; SEQUENTIAL [(I-J)=1] = 229; MEDIUM ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 869 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 783; INTRA-RESIDUE [I=J] = 4; SEQUENTIAL [(I-J)=1] = 229; MEDIUM RANGE [1<(I-J)<5] = 159; LONG RANGE [(I-J)>=5] = 333; HYDROGEN BOND CONSTRAINTS = 58 (2 PER H-BOND); NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE = 10.7; DIHEDRAL-ANGLE CONSTRAINTS = 86 (50 PHI, 36 PSI); TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 11.9; NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 4.6; NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0 ANG = 22.9; AVERAGE R.M.S. DISTANCE VIOLATION = 0.006 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 28. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 4.6; MAX NUMBER OF ANGLE VIOLATION = 7 DEG; AVERAGE R.M.S. ANGLE VIOLATION = 0.14 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C',O) = 0.61 ANG; ALL HEAVY ATOMS = 1.17 ANG; PROCHECK: MOST FAVORED REGIONS = 92%; ADDITIONAL ALLOWED REGIONS = 4%; GENEROUSLY ALLOWED REGIONS = 2%; DISALLOWED REGIONS = 2%.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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