BMRB: 10108

Solution Structure of DC1 Domain of PDI-like Hypothetical Protein from Arabidopsis thaliana

Authors

Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

PDI-like Hypothetical Protein At1g60420

Entity

1. PDI-like Hypothetical Protein At1g60420 (polymer, Thiol state: all other bound), 89 monomers, 10116.94 Da Detail

GSSGSSGTEE RLKEIEAKYD EIAKDWPKKV KHVLHEEHEL ELTRVQVYTC DKCEEEGTIW SYHCDECDFD LHAKCALNED TKESGPSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

10247.759 Da

Max. entity weight

10116.94 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	2:ZN1:ZN	1:CYS50:SG
2	na	sing	2:ZN1:ZN	1:CYS53:SG
3	na	sing	2:ZN1:ZN	1:HIS72:ND1
4	na	sing	2:ZN1:ZN	1:CYS75:SG
5	na	sing	2:ZN1:ZN	1:HIS35:ND1
6	na	sing	2:ZN1:ZN	1:HIS38:ND1
7	na	sing	2:ZN1:ZN	1:CYS64:SG
8	na	sing	2:ZN1:ZN	1:CYS67:SG

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Refine. method

Torsion Angle Dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.6 %, Completeness: 90.2 %, Completeness (bb): 86.2 % Detail

Download

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	90.2 % (904 of 1002)	90.4 % (472 of 522)	90.5 % (352 of 389)	87.9 % (80 of 91)
Backbone	86.2 % (457 of 530)	85.2 % (155 of 182)	86.6 % (226 of 261)	87.4 % (76 of 87)
Sidechain	93.9 % (521 of 555)	93.2 % (317 of 340)	94.8 % (200 of 211)	100.0 % (4 of 4)
Aromatic	100.0 % (78 of 78)	100.0 % (39 of 39)	100.0 % (37 of 37)	100.0 % (2 of 2)
Methyl	100.0 % (70 of 70)	100.0 % (35 of 35)	100.0 % (35 of 35)

1. PDI-like Hypothetical Protein At1g60420

GSSGSSGTEE RLKEIEAKYD EIAKDWPKKV KHVLHEEHEL ELTRVQVYTC DKCEEEGTIW SYHCDECDFD LHAKCALNED TKESGPSSG

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)

#	Name	Isotope labeling	Type	Concentration
1	DC1 Domain	[U-13C; U-15N]		1.05 mM
2	d-Tris-HCl		buffer	20 mM
3	NaCl		salt	100 mM
4	d-DTT		salt	1 mM
5	NaN3			0.02 %
6	ZnCl2			0.1 mM
7	H2O		solvent	90 %
8	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.09 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

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LACS Plot; CB

Referencing offset: -0.09 ppm, Outliers: 2 Detail

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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

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LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

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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

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LACS Plot; CO

Referencing offset: 0.01 ppm, Outliers: 4 Detail

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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

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Protein Blocks Logo

Calculated from 20 models in PDB: 1V5N, Strand ID: A Detail

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Release date

2008-08-28

Citation

Solution Structure of DC1 Domain of PDI-like Hypothetical Protein from Arabidopsis thaliana
Miyamoto, K., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.
Not known

Related entities 1. PDI-like Hypothetical Protein At1g60420, : 1 : 27 entities Detail

Interaction partners 1. PDI-like Hypothetical Protein At1g60420, : 1 interactors Detail

Experiments performed 2 experiments Detail