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BMRB: 11555

2RU9

Structure of the YAM domain of E. coli Transporter YajR

Authors

Liu, X., Feng, W.

Assembly

the YAM domain of E. coli Transporter YajR

Entity

1. the YAM domain of E. coli Transporter YajR (polymer, Thiol state: not present), 76 monomers, 8688.704 Da Detail

MGKEPPYVSS LRIEIPADIA ANEALKVRLL ETEGVKEVLI AEEEHSAYVK IDSKVTNRFE VEQAIRQALE HHHHHH

Formula weight

8688.704 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.1 %, Completeness: 83.6 %, Completeness (bb): 88.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.6 % (743 of 889)	81.6 % (377 of 462)	84.9 % (297 of 350)	89.6 % (69 of 77)
Backbone	88.7 % (399 of 450)	88.7 % (134 of 151)	88.5 % (200 of 226)	89.0 % (65 of 73)
Sidechain	80.1 % (411 of 513)	78.1 % (243 of 311)	82.8 % (164 of 198)	100.0 % (4 of 4)
Aromatic	37.0 % (20 of 54)	48.1 % (13 of 27)	25.9 % (7 of 27)
Methyl	94.8 % (91 of 96)	93.8 % (45 of 48)	95.8 % (46 of 48)

1. entity

MGKEPPYVSS LRIEIPADIA ANEALKVRLL ETEGVKEVLI AEEEHSAYVK IDSKVTNRFE VEQAIRQALE HHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

LACS Plot; CA

Referencing offset: 0.26 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.26 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.43 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2RU9, Strand ID: A Detail

Release date

2014-06-29

Citation

Atomic resolution structure of the E. coli YajR transporter YAM domain
Jiang, D., Zhang, X.C.
Biochem. Biophys. Res. Commun. (2014), 450, 929-935, PubMed 24952155 , DOI 10.1016/j.bbrc.2014.06.053 , Abstract

Related entities 1. the YAM domain of E. coli Transporter YajR, : 1 : 3 : 7 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

5 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

6 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	YAM		protein	1.2 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	natural abundance	solvent	10 %
4	sodium phosphate	natural abundance	buffer	50 mM
5	EDTA	natural abundance		1 mM
6	DTT	natural abundance		1 mM
7	sodium chloride	natural abundance	salt	150 mM

nullKeywords ferredoxin like