BMRB Entry 15864

Name: Solution structure of 1-112 fragment of human programmed cell death 5 protein
Published: 2009-05-18

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PDB ID: 2k6b
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15864
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of 1-112 fragment of human programmed cell death 5 protein PubMed: 19358820

Deposition date: 2008-07-07 Original release date: 2009-05-18

Authors: Feng, Yingang; Yao, Hongwei; Liu, Dongsheng; Wang, Jinfeng

Citation: Yao, Hongwei; Xu, Lanjun; Feng, Yingang; Liu, Dongsheng; Chen, Yingyu; Wang, Jinfeng. "Structure-function correlation of human programmed cell death 5 protein" Arch. Biochem. Biophys. 486, 141-149 (2009).

Assembly members:
pdcd5, polymer, 113 residues, 12692.453 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
pdcd5: GSADEELEALRRQRLAELQA KHGDPGDAAQQEAKHREAEM RNSILAQVLDQSARARLSNL ALVKPEKTKAVENYLIQMAR YGQLSEKVSEQGLIEILKKV SQQTEKTTTVKFN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	477
15N chemical shifts	114
1H chemical shifts	761

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	pdcd5	1

Entities:

Entity 1, pdcd5 113 residues - 12692.453 Da.

1

GLY

SER

ALA

ASP

GLU

LEU

GLU

ALA

LEU

2

ARG

GLN

ARG

LEU

ALA

GLU

LEU

GLN

ALA

3

LYS

HIS

GLY

ASP

PRO

GLY

ASP

ALA

GLN

4

GLN

GLU

ALA

LYS

HIS

ARG

GLU

ALA

GLU

MET

5

ARG

ASN

SER

ILE

LEU

ALA

GLN

VAL

LEU

ASP

6

GLN

SER

ALA

ARG

ALA

ARG

LEU

SER

ASN

LEU

7

ALA

LEU

VAL

LYS

PRO

GLU

LYS

THR

LYS

ALA

8

VAL

GLU

ASN

TYR

LEU

ILE

GLN

MET

ALA

ARG

9

TYR

GLY

GLN

LEU

SER

GLU

LYS

VAL

SER

GLU

10

GLN

GLY

LEU

ILE

GLU

ILE

LEU

LYS

VAL

11

SER

GLN

THR

GLU

LYS

THR

VAL

12

LYS

PHE

ASN

Samples:

sample_1: pdcd5, [U-13C; U-15N], 1.0-2.0 mM; acetic acid, [U-2H], 100 mM; sodium chloride 100 mM; DSS 0.01%; sodium azide 0.01%

sample_2: pdcd5, [U-13C], 1.0-2.0 mM; acetic acid, [U-2H], 100 mM; sodium chloride 100 mM; DSS 0.01%; sodium azide 0.01%

sample_conditions_1: ionic strength: 0.1 M; pH: 4.7; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

FELIX, Accelrys Software Inc. - data analysis, processing

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Bruker DMX 600 MHz

PDB	2CRU 2K6B
DBJ	BAJ20402
EMBL	CAG33215 CAH90780
GB	AAD11579 AAH15519 AAP35340 AAP36696 AAX36432
REF	NP_001125439 NP_001252621 NP_004699 XP_002762025 XP_003275098
SP	O14737 Q5RBT0

Biological Magnetic Resonance Data Bank