BMRB: 6955

Solution Structure of the gene product of E. coli gene ydhA

Authors

Shaw, G.S., Revington, M.J.

Assembly

Hypothetical protein ydhA

Entity

1. Hypothetical protein ydhA (polymer, Thiol state: all disulfide bound), 102 monomers, 11716.91 Da Detail

MGSSHHHHHH SSGLVPRGSH MQTDTLEYQC DEKPLTVKLN NPRQEVSFVY DNQLLHLKQG ISASGARYTD GIYVFWSKGD EATVYKRDRI VLNNCQLQNP QR

Formula weight

11716.91 Da

Entity Connection

disulfide 1 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS30:SG	1:CYS95:SG

Source organism

Escherichia coli

Exptl. method

NMR

Refine. method

simulated annealing, torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 80.4 %, Completeness: 69.8 %, Completeness (bb): 78.1 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	69.8 % (832 of 1192)	70.3 % (438 of 623)	68.6 % (313 of 456)	71.7 % (81 of 113)
Backbone	78.1 % (472 of 604)	79.2 % (164 of 207)	76.9 % (230 of 299)	79.6 % (78 of 98)
Sidechain	63.8 % (436 of 683)	65.9 % (274 of 416)	63.1 % (159 of 252)	20.0 % (3 of 15)
Aromatic	5.8 % (6 of 104)	9.6 % (5 of 52)	0.0 % (0 of 51)	100.0 % (1 of 1)
Methyl	90.2 % (83 of 92)	91.3 % (42 of 46)	89.1 % (41 of 46)

1. Hypothetical protein ydhA

MGSSHHHHHH SSGLVPRGSH MQTDTLEYQC DEKPLTVKLN NPRQEVSFVY DNQLLHLKQG ISASGARYTD GIYVFWSKGD EATVYKRDRI VLNNCQLQNP QR

Show sample condition

Sample

Pressure 1 atm, Temperature 298.0 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Hypothetical protein ydhA	[U-13C; U-15N]		0.5 mM
2	sodium phosphate			10 mM
3	NaCl			400 mM
4	dithiothreitol			10 mM
5	sodium azide			0.01 %
6	benzamidine			1 mM
7	H2O			90 %
8	D2O			10 %

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LACS Plot; CA

Referencing offset: -0.01 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	external	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.101329

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LACS Plot; CB

Referencing offset: -0.01 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	external	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.101329

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LACS Plot; HA

Referencing offset: -0.13 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	external	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.101329

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LACS Plot; CO

Referencing offset: 0.89 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	external	direct	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.101329

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Protein Blocks Logo

Calculated from 20 models in PDB: 2F09, Strand ID: A Detail

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Release date

2006-11-05

Citation

The solution structure of the protein ydhA from Escherichia coli
Revington, M.J., Semesi, A., Yee, A., Arrowsmith, C.H., Shaw, G.S.
J. Biomol. NMR (2006), 35, 295-300, PubMed 16937244 , DOI 10.1007/s10858-006-9032-y , Abstract

Related entities 1. Hypothetical protein ydhA, : 1 : 2 : 19 entities Detail

Interaction partners 1. Hypothetical protein ydhA, : 4 interactors Detail

Experiments performed 2 experiments Detail