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BMRB: 18283

2LRV

Assignment of E coli periplasmic protein YmgD

Authors

Wu, K., Inouye, M., Baum, J.

Assembly

YmgD dimer

Entity

1. YmgD dimer (polymer, Thiol state: all disulfide bound), 90 monomers, 9727.039 × 2 Da Detail

QDYNIKNGLP SETYITCAEA NEMAKTDSAQ VAEIVAVMGN ASVASRDLKI EQSPELSAKV VEKLNQVCAK DPQMLLITAI DDTMRAIGKK

Total weight

19454.078 Da

Max. entity weight

9727.039 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS17:SG	1:CYS68:SG
2	disulfide	sing	2:CYS17:SG	2:CYS68:SG

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.1 %, Completeness (bb): 95.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (906 of 1006)	88.7 % (463 of 522)	89.4 % (346 of 387)	100.0 % (97 of 97)
Backbone	95.9 % (512 of 534)	97.8 % (176 of 180)	93.6 % (250 of 267)	98.9 % (86 of 87)
Sidechain	84.4 % (472 of 559)	83.6 % (286 of 342)	85.0 % (176 of 207)	100.0 % (10 of 10)
Aromatic	62.5 % (10 of 16)	100.0 % (8 of 8)	25.0 % (2 of 8)
Methyl	88.6 % (101 of 114)	94.7 % (54 of 57)	82.5 % (47 of 57)

1. YmgD

QDYNIKNGLP SETYITCAEA NEMAKTDSAQ VAEIVAVMGN ASVASRDLKI EQSPELSAKV VEKLNQVCAK DPQMLLITAI DDTMRAIGKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

Protein Blocks Logo

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

Release date

2013-04-14

Citation

Solution structure of homodimeric periplasmic protein YmgD in E. coli
Wu, K., Masuda, H., Hsu, S.D., Baum, J., Inouye, M.
J. Biol. Chem.

Related entities 1. YmgD dimer, : 1 : 3 : 5 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

3 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

4 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

5 3D HN(CA)CO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

6 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

7 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

8 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

10 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

12 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

13 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5, Details double labeled sample

#	Name	Isotope labeling	Type	Concentration
1	YmgD	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	Sodium acetate	natural abundance		100 mM
5	NaCl	natural abundance		50 mM

nullKeywords dimer, periplasm, YmgD