BMRBj - BMREntryMaster

Found 1 Document (0.598 seconds)

BMRB: 19256

3RFZ

NMR assignments and backbone amide relaxation data (T1-T2) for the complex of the FimH adhesin carbohydrate-binding domain with heptyl-mannose

Authors

Vanwetswinkel, S., Van Nuland, N.A.

Assembly

FimH -heptyl-mannose complex

Entity

1. FIMH (polymer, Thiol state: all disulfide bound), 158 monomers, 16907.74 Da Detail

FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSN FSGTVKYSGS SYPFPTTSET PRVVYNSRTD KPWPVALYLT PVSSAGGVAI KAGSLIAVLI LRQTNNYNSD DFQFVWNIYA NNDVVVPT

2. Heptyl Alpha-D-mannopyrannoside (non-polymer), 278.342 Da

Total weight

17186.082 Da

Max. entity weight

16907.74 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS44:SG

Source organism

Escherichia coli

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.9 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.9 % (1581 of 1758)	89.9 % (801 of 891)	87.7 % (612 of 698)	99.4 % (168 of 169)
Backbone	96.6 % (896 of 928)	97.2 % (310 of 319)	95.0 % (438 of 461)	100.0 % (148 of 148)
Sidechain	84.2 % (821 of 975)	85.8 % (491 of 572)	81.2 % (310 of 382)	95.2 % (20 of 21)
Aromatic	33.3 % (56 of 168)	36.9 % (31 of 84)	28.0 % (23 of 82)	100.0 % (2 of 2)
Methyl	99.0 % (202 of 204)	100.0 % (102 of 102)	98.0 % (100 of 102)

1. FIMH

FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSN FSGTVKYSGS SYPFPTTSET PRVVYNSRTD KPWPVALYLT PVSSAGGVAI KAGSLIAVLI LRQTNNYNSD DFQFVWNIYA NNDVVVPT

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000, Details FimH_protonated 0.001000 M, heptyl-mannose 0.0013 M, sodium phosphate 0.020000 M, sodium chloride 0.100000 M

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000, Details FimH_protonated 0.0011M, heptyl-mannose 0.0013 M, sodium phosphate 0.020000 M, sodium

#	Name	Isotope labeling	Concentration
7	FIMH	[U-100% 15N]	1.1 mM
8	heptyl alpha-D-mannopyranoside (heptyl-mannose)	natural abundance	1.3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	93 %
12	D2O	natural abundance	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	HDO	proton	4.7 ppm	internal	indirect	1.0

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	HDO	proton	4.7 ppm	internal	indirect	1.0

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	HDO	proton	4.7 ppm	internal	indirect	1.0

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	HDO	proton	4.7 ppm	internal	indirect	1.0

Referencing offset: 0.72 ppm, Outliers: 3 Detail

Heteronucl. T₁

131 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600 MHz, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000 Detail

Heteronucl. T₂

127 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000 Detail

Heteronucl. T₁/T₂

127 T₁/T₂ values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000 Detail

Release date

2014-02-12

Citation

Study of the structural and dynamic effects in the FimH adhesin upon α-d-heptyl mannose binding
Vanwetswinkel, S., Volkov, A.N., Sterckx, Y.G.J., Garcia-Pino, A., Buts, L., Vranken, W.F., Bouckaert, J., Roy, R., Wyns, L., van Nuland, N.A.J.
J. Med. Chem. (2014), 57, 1416-1427, PubMed 24476493 , DOI 10.1021/jm401666c , Abstract

Related entities 1. FIMH, : 1 : 63 : 3 : 6 : 26 entities Detail

Interaction partners 1. FIMH, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Direct-Drive - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000, Details FimH_protonated 0.001000 M, heptyl-mannose 0.0013 M, sodium phosphate 0.020000 M, sodium chloride 0.100000 M

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

2 2D 1H-13C HSQC

Instrument

Varian Direct-Drive - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

3 3D HNCA

Instrument

Varian Direct-Drive - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

4 3D HNCO

Instrument

Varian Direct-Drive - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

5 3D HNCOCA

Instrument

Varian Direct-Drive - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

6 3D CCH-TOCSY

Instrument

Varian Direct-Drive - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

7 2D (HB)CB(CGCD)HD

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

8 2D (HB)CB(CGCDCE)HE

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	FIMH	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	0.02 M
3	sodium chloride	natural abundance	0.1 M
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %
6	heptyl-mannose	natural abundance	1.3 mM

12 2D 1H-15N HSQC (inversion recovery)

Instrument

Varian Direct-Drive - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1.000 atm, Temperature 298.000 K, pH 6.000, Details FimH_protonated 0.0011M, heptyl-mannose 0.0013 M, sodium phosphate 0.020000 M, sodium

#	Name	Isotope labeling	Concentration
7	FIMH	[U-100% 15N]	1.1 mM
8	heptyl alpha-D-mannopyranoside (heptyl-mannose)	natural abundance	1.3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	93 %
12	D2O	natural abundance	7 %

13 2D 1H-15N HSQC (CPMG)

Instrument

Varian Direct-Drive - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	FIMH	[U-100% 15N]	1.1 mM
8	heptyl alpha-D-mannopyranoside (heptyl-mannose)	natural abundance	1.3 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	93 %
12	D2O	natural abundance	7 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl T1 relaxation data, Heteronucl T2 relaxation data	bmr19256_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)
1:3:CYS:SG	1:44:CYS:SG	oxidized, CA 56.15115, CB 51.56894 ppm	oxidized, CA 55.93683, CB 49.96361 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr19256_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	1799		100.0 (chain: 1, length: 158)
1	Chemical shift references	chemical_shift_reference_1	Warning	1		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 158, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTD

-------110-------120-------130-------140-------150--------
KPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT

Total number of assignments
- ¹³C chemical shifts: 622
- ¹H chemical shifts: 1006
- ¹⁵N chemical shifts: 171

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	THR	HG1	5.35797
7	ASN	CG	177.6559
19	ASN	CG	176.22275
23	ASN	CG	176.95209
29	ASN	CG	176.76145
32	GLN	CD	180.67169
33	ASN	CG	175.49533
41	GLN	CD	178.27272
59	GLN	CD	177.5151
70	ASN	CG	176.91623
86	THR	HG1	6.54801
96	ASN	CG	177.11306
143	GLN	CD	180.31146
147	ASN	CG	175.24614
151	ASN	CG	175.48133
152	ASN	CG	176.41501

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	698	608	87.1
¹H chemical shifts	891	800	89.8
¹⁵N chemical shifts	173	171	98.8

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	316	304	96.2
¹H chemical shifts	319	313	98.1
¹⁵N chemical shifts	148	147	99.3

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	382	304	79.6
¹H chemical shifts	572	487	85.1
¹⁵N chemical shifts	25	24	96.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	102	99	97.1
¹H chemical shifts	102	102	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	82	19	23.2
¹H chemical shifts	84	21	25.0
¹⁵N chemical shifts	2	2	100.0

Redox state of CYS
Peptide bond of PRO
Tautomeric state of HIS
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 bacterial adhesin, carbohydrate, CELL ADHESION, NMR, urinary tract infection

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Found 1 Document (0.598 seconds)

BMRB: 19256

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. FIMH, : 1 : 63 : 3 : 6 : 26 entities Detail

Interaction partners 1. FIMH, : 4 interactors Detail

Experiments performed 13 experiments Detail

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Chemical shift validation 4 contents Detail