- PDB-1m94: Solution Structure of the Yeast Ubiquitin-Like Modifier Protein Hub1 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1m94
Title
Solution Structure of the Yeast Ubiquitin-Like Modifier Protein Hub1
Components
Protein YNR032c-a
Keywords
STRUCTURAL 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 tag activity / nucleus / cytoplasm Similarity search - Function
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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 15N-separated NOESY
1
2
1
HNHA
1
3
1
3D 13C-separated NOESY
1
4
2
4D 13C/15N-separated NOESY
NMR details
Text: 1H-13C HSQC on 10% C13, U-15N sample for stereospecific assignments of Leu and Val
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1-3 mM Hub1, U-15N, 13C, NaOAc, pH 5.0
90% H2O, 10% D20
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1-3 mM Hub1, U-15N, 13C, NaOAc, pH* 4.6
99% H2O, 1% D20
3
1-3 mM Hub1, U-15N, NaOAc, pH 5.0
90% H2O, 10% D20
4
1-3 mM Hub1, U-15N, 10%-13C, NaOAc, pH 5.0
90% H2O, 10% D20
Sample conditions
Ionic strength: 10 mM NaOAc, 300 mM NaCl / pH: 5.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
800
1
Varian INOVA
Varian
INOVA
750
2
Varian INOVA
Varian
INOVA
600
3
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Processing
NMR software
Name
Version
Developer
Classification
X-PLOR
3.84
Brunger, A.T.
structuresolution
Felix
98
MSI
processing
VNMR
6.1C
Varian
collection
Sparky
3.98
Goddard, Kneller
dataanalysis
X-PLOR
3.84
Brunger, A.T.
refinement
Refinement
Method: 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 representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20
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