BMRBj - BMREntryMaster

Found 1 Document (6.59 seconds)

BMRB: 6102

1RWU

Solution structure of conserved protein YbeD from E. coli

Authors

Kozlov, G., Gehring, K.

Assembly

Hypothetical UPF0250 protein ybeD

Entity

1. Hypothetical UPF0250 protein ybeD (polymer, Thiol state: not present), 109 monomers, 12402.91 × 2 Da Detail

MGTSHHHHHH SSGRENLYFQ GHMKTKLNEL LEFPTPFTYK VMGQALPELV DQVVEVVQRH APGDYTPTVK PSSKGNYHSV SITINATHIE QVETLYEELG KIDIVRMVL

Total weight

24805.82 Da

Max. entity weight

12402.91 Da

Source organism

Escherichia coli

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.7 %, Completeness: 50.4 %, Completeness (bb): 63.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	50.4 % (644 of 1279)	55.8 % (369 of 661)	38.1 % (193 of 506)	73.2 % (82 of 112)
Backbone	63.4 % (407 of 642)	71.7 % (157 of 219)	53.1 % (170 of 320)	77.7 % (80 of 103)
Sidechain	42.5 % (314 of 739)	48.0 % (212 of 442)	34.7 % (100 of 288)	22.2 % (2 of 9)
Aromatic	14.5 % (16 of 110)	29.1 % (16 of 55)	0.0 % (0 of 55)
Methyl	50.8 % (63 of 124)	79.0 % (49 of 62)	22.6 % (14 of 62)

1. YbeD

MGTSHHHHHH SSGRENLYFQ GHMKTKLNEL LEFPTPFTYK VMGQALPELV DQVVEVVQRH APGDYTPTVK PSSKGNYHSV SITINATHIE QVETLYEELG KIDIVRMVL

Show sample condition

Sample

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	YbeD	[U-13C; U-15N]	2 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.7 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.7 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
¹³C	DSS	methyl protons	null	indirect	0.2514495

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 1RWU, Strand ID: A Detail

Release date

2005-01-19

Citation

Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains
Kozlov, G., Elias, D., Semesi, A., Cygler, M., Gehring, K.
J. Bacteriol. (2004), 186, 8083-8088, PubMed 15547281 , DOI 10.1128/JB.186.23.8083-8088.2004 , Abstract

Related entities 1. Hypothetical UPF0250 protein ybeD, : 1 : 33 entities Detail

Experiments performed 3 experiments Detail

1 3D 15N-separated NOESY

Instrument

Model Bruker DRX (500 MHz)

Sample #1

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	YbeD	[U-13C; U-15N]	2 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
7	YbeD	[U-15N]	2 mM
8	phosphate buffer	natural abundance	50 mM
9	NaCl	natural abundance	300 mM
10	sodium azide	natural abundance	0.1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Concentration
13	YbeD	2 mM
14	phosphate buffer	50 mM
15	NaCl	300 mM
16	sodium azide	0.1 mM
17	D2O	100 %

2 HNHA

Instrument

Model Bruker DRX (500 MHz)

Sample #1

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	YbeD	[U-13C; U-15N]	2 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
7	YbeD	[U-15N]	2 mM
8	phosphate buffer	natural abundance	50 mM
9	NaCl	natural abundance	300 mM
10	sodium azide	natural abundance	0.1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Concentration
13	YbeD	2 mM
14	phosphate buffer	50 mM
15	NaCl	300 mM
16	sodium azide	0.1 mM
17	D2O	100 %

3 2D NOESY

Instrument

Model Bruker DRX (500 MHz)

Sample #1

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
1	YbeD	[U-13C; U-15N]	2 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM
4	sodium azide	natural abundance	0.1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Isotope labeling	Concentration
7	YbeD	[U-15N]	2 mM
8	phosphate buffer	natural abundance	50 mM
9	NaCl	natural abundance	300 mM
10	sodium azide	natural abundance	0.1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Pressure 1 atm, Temperature 298 (±0.5) K, pH 6.3 (±0.1)

#	Name	Concentration
13	YbeD	2 mM
14	phosphate buffer	50 mM
15	NaCl	300 mM
16	sodium azide	0.1 mM
17	D2O	100 %

nullKeywords mixed alpha-beta fold, Structural Genomics

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Found 1 Document (6.59 seconds)

BMRB: 6102

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Hypothetical UPF0250 protein ybeD, : 1 : 33 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3