BMRB: 11091

Solution structure of the C-terminal PapD-like domain from human HYDIN protein

Authors

Li, H., Sato, M., Koshiba, S., Watanabe, S., Harada, T., Kigawa, T., Yokoyama, S.

Assembly

HYDIN protein

Entity

1. HYDIN protein (polymer, Thiol state: all free), 112 monomers, 11823.38 Da Detail

GSSGSSGPKI HFNFELLDIG KVFTGSAHCY EAILYNKGSI DALFNMTPPT SALGACFVFS PKEGIIEPSG VQAIQISFSS IILGNFEEEF LVNVNGSPEP VKLTIRGCVI GP

Formula weight

11823.38 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 97.2 %, Completeness (bb): 96.0 % Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	97.2 % (1230 of 1266)	97.2 % (633 of 651)	97.2 % (489 of 503)	96.4 % (108 of 112)
Backbone	96.0 % (630 of 656)	96.5 % (221 of 229)	95.7 % (309 of 323)	96.2 % (100 of 104)
Sidechain	98.2 % (696 of 709)	97.6 % (412 of 422)	98.9 % (276 of 279)	100.0 % (8 of 8)
Aromatic	100.0 % (114 of 114)	100.0 % (57 of 57)	100.0 % (57 of 57)
Methyl	100.0 % (128 of 128)	100.0 % (64 of 64)	100.0 % (64 of 64)

1. PapD domain

GSSGSSGPKI HFNFELLDIG KVFTGSAHCY EAILYNKGSI DALFNMTPPT SALGACFVFS PKEGIIEPSG VQAIQISFSS IILGNFEEEF LVNVNGSPEP VKLTIRGCVI GP

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 (±0.001) atm, Temperature 296 (±0.1) K, pH 7.0 (±0.05), Details 1.13mM PapD domain [U-15N,13C], 20mM d-Tris-HCl(pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PapD domain	[U-13C; U-15N]	protein	1.13 mM
2	TRIS	[U-2H]	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	DTT	[U-2H]	salt	1 mM
5	sodium azide	natural abundance	salt	0.02 %
6	H2O		solvent	90 %
7	D2O		solvent	10 %

Hide sample codition

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Hide chemical shift referencing parameters

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Hide chemical shift referencing parameters

LACS Plot; HA

Referencing offset: -0.2 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Hide chemical shift referencing parameters

LACS Plot; CO

Referencing offset: 0.54 ppm, Outliers: 4 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Hide chemical shift referencing parameters

Protein Blocks Logo

Calculated from 20 models in PDB: 2E6J, Strand ID: A Detail

---

Release date

2011-01-18

Citation

Solution structure of the C-terminal PapD-like domain from human HYDIN protein
Li, H., Sato, M., Koshiba, S., Watanabe, S., Harada, T., Kigawa, T., Yokoyama, S.

Related entities 1. HYDIN protein, : 1 : 1 : 9 entities Detail

Interaction partners 1. HYDIN protein, : 1 interactors Detail

Experiments performed 2 experiments Detail