BMRB Entry 15562

Name: Solution Structure of S. cerevisiae PDCD5-like Protein Ymr074cp
Published: 2009-06-17

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PDB ID: 2jxn
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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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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(+)

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
coupling_constants
- coupling_constant_list_1
RDCs
- RDC_list_1
- RDC_list_2
order_parameters
- order_parameters
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
- heteronuclear_T1_list_2
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
- heteronuclear_T2_list_2
heteronucl_NOEs
- heteronuclear_noe_list_1
- Heteronuclear_noe_list_2

Data type	Count
1H chemical shifts	703
13C chemical shifts	466
15N chemical shifts	118
coupling constants	58
residual dipolar couplings	161
heteronuclear NOE values	179
T1 relaxation values	175
T2 relaxation values	173
order parameters	43

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	MSL_1	2
3	MSL_2	2

Entities:

Entity 1, entity_1 127 residues - 12577.217 Da.

Residues 117-127 represent a his tag

1

MET

ASP

PRO

GLU

LEU

GLN

ALA

ILE

ARG

GLU

2

ALA

ARG

LEU

ALA

GLN

LEU

LYS

ASN

SER

3

GLY

THR

ASN

GLY

ASP

ARG

ASN

SER

GLY

4

ALA

ASN

GLY

GLU

ASN

SER

ALA

5

PRO

VAL

GLY

ALA

ILE

ALA

ASN

PHE

LEU

6

GLU

PRO

GLN

ALA

LEU

GLU

ARG

LEU

SER

ARG

7

VAL

ALA

LEU

VAL

ARG

ASP

ARG

ALA

GLN

8

ALA

VAL

GLU

THR

TYR

LEU

LYS

LEU

ILE

9

ALA

THR

ASN

VAL

THR

HIS

LYS

ILE

THR

10

GLU

ALA

GLU

ILE

VAL

SER

ILE

LEU

ASN

GLY

11

ILE

ALA

LYS

GLN

ASN

SER

GLN

ASN

12

SER

LYS

ILE

PHE

GLU

ALA

LEU

13

GLU

HIS

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_5	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_6	anisotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCANH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HBHA(CBCACO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 15N-edited-NOESY-HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 13C-edited-NOESY-HSQC	sample_2	isotropic	sample_conditions_1
H-D exchange	sample_2	isotropic	sample_conditions_2
NMR relaxation	sample_5	isotropic	sample_conditions_1
NMR relaxation	sample_5	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_7	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_8	isotropic	sample_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

PDB	2FH0 2JXN
DBJ	GAA25515
EMBL	CAA88799 CAY81892
GB	AHY76530 AJP40773 AJS61942 AJS62378 AJS62816
REF	NP_013790
SP	Q04773
TPG	DAA09972
AlphaFold	Q04773