BMRB: 11114

The solution structure of the second thioredoxin-like domain of human Protein disulfide-isomerase

Authors

Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

Protein disulfide-isomerase

Entity

1. Protein disulfide-isomerase (polymer, Thiol state: all free), 121 monomers, 13234.67 Da Detail

GSSGSSGPVK VLVGKNFEDV AFDEKKNVFV EFYAPWCGHC KQLAPIWDKL GETYKDHENI VIAKMDSTAN EVEAVKVHSF PTLKFFPASA DRTVIDYNGE RTLDGFKKFL ESGGQSGPSS G

Formula weight

13234.67 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.9 %, Completeness: 94.4 %, Completeness (bb): 93.0 % Detail

Download

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

Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	94.4 % (1311 of 1389)	94.3 % (678 of 719)	96.0 % (524 of 546)	87.9 % (109 of 124)
Backbone	93.0 % (664 of 714)	94.0 % (233 of 248)	94.3 % (331 of 351)	87.0 % (100 of 115)
Sidechain	96.0 % (753 of 784)	94.5 % (445 of 471)	98.4 % (299 of 304)	100.0 % (9 of 9)
Aromatic	98.7 % (148 of 150)	98.7 % (74 of 75)	98.6 % (72 of 73)	100.0 % (2 of 2)
Methyl	100.0 % (110 of 110)	100.0 % (55 of 55)	100.0 % (55 of 55)

1. Thioredoxin like domain

GSSGSSGPVK VLVGKNFEDV AFDEKKNVFV EFYAPWCGHC KQLAPIWDKL GETYKDHENI VIAKMDSTAN EVEAVKVHSF PTLKFFPASA DRTVIDYNGE RTLDGFKKFL ESGGQSGPSS G

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 1.2mM thioredoxin like domain [U-15N,13C]; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Thioredoxin like domain	[U-13C; U-15N]	protein	1.2 mM
2	d-Tris-HCl	[U-2H]	buffer	20 mM
3	sodium chloride	natural abundance	salt	100 mM
4	d-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: -0.22 ppm, Outliers: 3 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: -0.22 ppm, Outliers: 3 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: 0.03 ppm, Outliers: 2 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: 0.3 ppm, Outliers: 2 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: 1X5C, Strand ID: A Detail

---

Release date

2011-02-17

Citation

Solution structure of the bb' domains of human protein disulfide isomerase
Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.
FEBS J. (2009), 276, 1440-1449, PubMed 19187238 , DOI 10.1111/j.1742-4658.2009.06884.x , Abstract

Related entities 1. Protein disulfide-isomerase, : 1 : 9 : 306 entities Detail

Interaction partners 1. Protein disulfide-isomerase, : 82 interactors Detail

Experiments performed 2 experiments Detail