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Biological Magnetic Resonance Data Bank


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BMRB Entry 15562

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15562
MolProbity Validation Chart

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Title: Solution Structure of S. cerevisiae PDCD5-like Protein Ymr074cp   PubMed: 19469552

Deposition date: 2007-11-25 Original release date: 2009-06-17

Authors: Hong, Jingjun; Zhang, Jiahai; Liu, Zhijun; Shi, Yunyu; Wu, Jihui

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).

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
N116: MDPELQAIREARLAQLKNNS GGTNGDRNSGANNGGGENSA PVGAAIANFLEPQALERLSR VALVRRDRAQAVETYLKKLI ATNNVTHKITEAEIVSILNG IAKQQNSQNNSKIIFEAAAL EHHHHHH

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
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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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts