BMRB: 11216

Solution structure of the third PDZ domain of PDZ domain containing protein 1

Authors

Qin, X., Nagashima, T., Hayashi, F., Yokoyama, S.

Assembly

PDZ domain containing protein 1

Entity

1. PDZ domain containing protein 1 (polymer, Thiol state: not present), 102 monomers, 10473.58 Da Detail

GSSGSSGRVV VIKKGSNGYG FYLRAGPEQK GQIIKDIEPG SPAEAAGLKN NDLVVAVNGK SVEALDHDGV VEMIRKGGDQ TTLLVLDKEA ESIYSLSGPS SG

Formula weight

10473.58 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.1 %, Completeness: 95.5 %, Completeness (bb): 94.0 % Detail

Download

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

Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	95.5 % (1047 of 1096)	94.7 % (538 of 568)	96.9 % (410 of 423)	94.3 % (99 of 105)
Backbone	94.0 % (568 of 604)	92.1 % (199 of 216)	95.5 % (277 of 290)	93.9 % (92 of 98)
Sidechain	97.2 % (562 of 578)	96.3 % (339 of 352)	98.6 % (216 of 219)	100.0 % (7 of 7)
Aromatic	100.0 % (38 of 38)	100.0 % (19 of 19)	100.0 % (19 of 19)
Methyl	100.0 % (114 of 114)	100.0 % (57 of 57)	100.0 % (57 of 57)

1. PDZ domain

GSSGSSGRVV VIKKGSNGYG FYLRAGPEQK GQIIKDIEPG SPAEAAGLKN NDLVVAVNGK SVEALDHDGV VEMIRKGGDQ TTLLVLDKEA ESIYSLSGPS SG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.05), Details 1.14mM 13C,15N-labeled {protein;} 20mM {d-Tris-HCl(pH7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} {90%H2O;} 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PDZ domain	[U-13C; U-15N]	protein	1.14 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	H2O		solvent	90 %
7	D2O		solvent	10 %

Hide sample codition

LACS Plot; CA

Referencing offset: -0.12 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: -0.12 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: -0.05 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: 0.23 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: 2D90, Strand ID: A Detail

---

Release date

2011-07-20

Citation

Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase
Qin, X., Nagashima, T., Hayashi, F., Yokoyama, S.
J. Biomol. NMR (2005), 32, 209-218, PubMed 16132821 , DOI 10.1007/s10858-005-7333-1 , Abstract

Related entities 1. PDZ domain containing protein 1, : 1 : 247 entities Detail

Interaction partners 1. PDZ domain containing protein 1, : 12 interactors Detail

Experiments performed 2 experiments Detail