BMRB Entry 15562

Title:
Solution Structure of S. cerevisiae PDCD5-like Protein Ymr074cp
Deposition date:
2007-11-25
Original release date:
2009-06-17
Authors:
Hong, Jingjun; Zhang, Jiahai; Liu, Zhijun; Shi, Yunyu; Wu, Jihui
Citation:

Citation: Hong, Jingjun; Zhang, Jiahai; Liu, Zhijun; Qin, Su; Wu, Jihui; Shi, Yunyu. "Solution structure of S. cerevisiae PDCD5-like protein and its promoting role in H(2)O(2)-induced apoptosis in yeast."  Biochemistry 48, 6824-6834 (2009).
PubMed: 19469552

Assembly members:

Assembly members:
N116, polymer, 127 residues, 12577.217 Da.
S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate, non-polymer, 264.385 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: SACCHAROMYCES CEREVISIAE

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PET-22B(+)

Data typeCount
1H chemical shifts703
13C chemical shifts466
15N chemical shifts118
coupling constants58
residual dipolar couplings161
heteronuclear NOE values179
T1 relaxation values175
T2 relaxation values173
order parameters43

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2MSL_12
3MSL_22

Entities:

Entity 1, entity_1 127 residues - 12577.217 Da.

Residues 117-127 represent a his tag

1   METASPPROGLULEUGLNALAILEARGGLU
2   ALAARGLEUALAGLNLEULYSASNASNSER
3   GLYGLYTHRASNGLYASPARGASNSERGLY
4   ALAASNASNGLYGLYGLYGLUASNSERALA
5   PROVALGLYALAALAILEALAASNPHELEU
6   GLUPROGLNALALEUGLUARGLEUSERARG
7   VALALALEUVALARGARGASPARGALAGLN
8   ALAVALGLUTHRTYRLEULYSLYSLEUILE
9   ALATHRASNASNVALTHRHISLYSILETHR
10   GLUALAGLUILEVALSERILELEUASNGLY
11   ILEALALYSGLNGLNASNSERGLNASNASN
12   SERLYSILEILEPHEGLUALAALAALALEU
13   GLUHISHISHISHISHISHIS

Entity 2, MSL_1 - C10 H18 N O3 S2 - 264.385 Da.

1   MTN

Samples:

sample_4: N116 A7C, [U-100% 15N], 0.2 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%; 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate 0.2 mM; ascorbate 1 mM

sample_1: N116, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%

sample_3: N116 A7C, [U-100% 15N], 0.2 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%; 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate 0.2 mM

sample_2: N116, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 100%

sample_5: N116, [U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%

sample_6: N116, [U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%; polyacrylamide gel 7 or 8%

sample_7: N116 A11C, [U-100% 15N], 0.2 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%; 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate 0.2 mM

sample_8: N116 A11C, [U-100% 15N], 0.2 mM; sodium phosphate 20 mM; sodium chloride 50 mM; EDTA 1 mM; D2O, [U-100% 2H], 10%; H2O 90%; 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate 0.2 mM; ascorbate 1 mM

sample_conditions_1: temperature: 298 K; pH: 6.0; pressure: 1 atm

sample_conditions_2: temperature: 295 K; pH: 6.0; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_5isotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_6anisotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D C(CO)NH-TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CBCACO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NH-TOCSYsample_1isotropicsample_conditions_1
3D 15N-edited-NOESY-HSQCsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 13C-edited-NOESY-HSQCsample_2isotropicsample_conditions_1
H-D exchangesample_2isotropicsample_conditions_2
NMR relaxationsample_5isotropicsample_conditions_1
NMR relaxationsample_5isotropicsample_conditions_1
2D 1H-15N HSQCsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_8isotropicsample_conditions_1

Software:

NMRPipe v2.2, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.110, Goddard - peak picking, chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - data analysis

X-PLOR_NIH v2.18, Schwieters, Kuszewski, Tjandra and Clore - structure solution, refinement

Procheck, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th - geometry optimization

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

Related Database Links:

PDB
DBJ GAA25515
EMBL CAA88799 CAY81892
GB AHY76530 AJP40773 AJS61942 AJS62378 AJS62816
REF NP_013790
SP Q04773
TPG DAA09972
AlphaFold Q04773

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks