BMRBj - BMREntryMaster

Found 1 Document (1.543 seconds)

BMRB: 7179

2JVU

Dispersin Solution Structure

Authors

Velarde, J.J., Varney, K.M., Inman, K.G., Weber, D.J., Nataro, J.P.

Assembly

Dispersin, Aap

Entity

1. Dispersin, Aap (polymer, Thiol state: all disulfide bound), 104 monomers, 11309.25 Da Detail

GGSGWNADNV DPSQCIKQSG VQYTYNSGVS VCMQGLNEGK VRGVSVSGVF YYNDGTTSNF KGVVTPSTPV NTNQDINKTN KVGVQKYRAL TEWVGSRSHH HHHH

Formula weight

11309.25 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS15:SG	1:CYS32:SG

Source organism

Escherichia coli

Exptl. method

Refine. method

DISTANCE GEOMETRY, SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.2 %, Completeness: 81.3 %, Completeness (bb): 91.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.3 % (935 of 1150)	77.2 % (457 of 592)	87.2 % (383 of 439)	79.8 % (95 of 119)
Backbone	91.3 % (564 of 618)	90.8 % (198 of 218)	91.6 % (274 of 299)	91.1 % (92 of 101)
Sidechain	73.2 % (456 of 623)	69.3 % (259 of 374)	84.0 % (194 of 231)	16.7 % (3 of 18)
Aromatic	45.4 % (49 of 108)	46.3 % (25 of 54)	42.3 % (22 of 52)	100.0 % (2 of 2)
Methyl	97.8 % (90 of 92)	97.8 % (45 of 46)	97.8 % (45 of 46)

1. Dispersin, Aap

GGSGWNADNV DPSQCIKQSG VQYTYNSGVS VCMQGLNEGK VRGVSVSGVF YYNDGTTSNF KGVVTPSTPV NTNQDINKTN KVGVQKYRAL TEWVGSRSHH HHHH

Show sample condition

Sample

Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

LACS Plot; CA

Referencing offset: 0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.19 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2006-07-13

Citation

Solution structure of the novel dispersin protein of enteroaggregative Escherichia coli
Velarde, J.J., Varney, K.M., Farfan, M., Dudley, E., Inman, K.G., Fletcher, J., Weber, D.J., Nataro, J.P.
Mol. Microbiol. (2007), 66, 1123-1135, PubMed 17986189 , DOI 10.1111/j.1365-2958.2007.05985.x , Abstract

Related entities 1. Dispersin, Aap, : 1 : 4 entities Detail

Experiments performed 16 experiments Detail

1 2D NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

2 2D TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

3 3D 13C-separated NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

4 3D 15N-separated NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

5 4D 13C-separated NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

6 4D 13C/15N-separated NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

7 3D 15N-edited HOHAHA-HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

8 3D 15N edited HMQC-NOESY-HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

9 3D 15N HNHA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

10 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

11 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

12 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

13 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

14 3D HCA(CO)N

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

15 IPAP-HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

16 3D HN(CO)CA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Dispersin, Aap	[U-15N; U-13C]		1 mM
2	Phosphate			45 mM
3	NaCl			45 mM
4	EDTA			0.2 mM
5	NaN3			0.2 mM
6	DTT			0.1 mM
7	H2O			90 %
8	D2O			10 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr7179_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:15:CYS:SG	1:32:CYS:SG	oxidized, CA 53.19, CB 37.72 ppm	oxidized, CA 56.47, CB 37.49 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr7179_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chemical_shift_set_1	Warning	1015		93.3 (chain: 1, length: 104)

Assigned chemical shifts

Saveframe: chemical_shift_set_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 104, Sequence coverage: 93.3%
- Total number of assignments
  - ¹³C chemical shifts: 380
  - ¹H chemical shifts: 539
  - ¹⁵N chemical shifts: 96
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords Beta sandwich