- PDB-7en4: Multi-state structure determination and dynamics analysis elucida... -
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Basic information
Entry
Database: PDB / ID: 7en4
Title
Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
Components
Ubiquitin carboxyl-terminal hydrolase YUH1
Keywords
HYDROLASE / PROTEIN solution NMR
Function / homology
Function and homology information
UCH proteinases / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin recycling / Neddylation / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cytoplasm Similarity search - Function
BMRB: 36420Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
2 mM [U-100% 15N] ubiquitin hydrolase, 90% H2O/10% D2O
15N_sample
90% H2O/10% D2O
solution
3
2 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase, 90% H2O/10% D2O
ILVFYW_selective_sample
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
2mM
ubiquitinhydrolase
[U-100% 13C; U-100% 15N; U-50% 2H]
1
2mM
ubiquitinhydrolase
[U-100% 15N]
2
2mM
ubiquitinhydrolase
Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled
3
Sample conditions
Ionic strength: 100 mM / Label: conditions_1 / pH: 6 / Pressure: AMBIENT Pa / Temperature: 303 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
600
1
Bruker AVANCE III
Bruker
AVANCEIII
600
2
Bruker AVANCE III
Bruker
AVANCEIII
700
3
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Processing
NMR software
Name
Version
Developer
Classification
CYANA
3.99.0
Guntert, MumenthalerandWuthrich
structurecalculation
Azara
2.8.1
Boucher
processing
CcpNmr Analysis
2.5.0
CCPN
chemicalshiftassignment
TopSpin
3.5
BrukerBiospin
collection
OPAL
1.4
Luginbuhl, Guntert, BilleterandWuthrich
refinement
CcpNmr Analysis
2.5.0
CCPN
peakpicking
Refinement
Method: energy minimization / Software ordinal: 5
NMR representative
Selection criteria: closest the center of the largest cluster
NMR ensemble
Conformer selection criteria: structures randomly selected from each of five clusters Conformers calculated total number: 20 / Conformers submitted total number: 20
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