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Found 1 Document (2.42 seconds)

BMRB: 34048

5M0A

Solution structure of isolated 15th Fibronectin III domain from human fibronectin

Authors

Waltho, J.P., Cliff, M.J., Blumson, E., Humphries, M.

Assembly

Fibronectin

Entity

1. Fibronectin (polymer, Thiol state: all free), 86 monomers, 9336.161 Da Detail

NASTGQEALS QTTISWAPFQ DTSEYIISCH PVGTDEEPLQ FRVPGTSTSA TLTGLTRGAT YNIIVEALKD QQRHKVREEV VTVGNS

Formula weight

9336.161 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.8 %, Completeness (bb): 84.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.8 % (850 of 947)	97.1 % (471 of 485)	78.1 % (289 of 370)	97.8 % (90 of 92)
Backbone	84.6 % (430 of 508)	99.4 % (173 of 174)	69.4 % (175 of 252)	100.0 % (82 of 82)
Sidechain	96.3 % (500 of 519)	95.8 % (298 of 311)	98.0 % (194 of 198)	80.0 % (8 of 10)
Aromatic	89.3 % (50 of 56)	92.9 % (26 of 28)	85.2 % (23 of 27)	100.0 % (1 of 1)
Methyl	100.0 % (104 of 104)	100.0 % (52 of 52)	100.0 % (52 of 52)

1. Fibronectin

NASTGQEALS QTTISWAPFQ DTSEYIISCH PVGTDEEPLQ FRVPGTSTSA TLTGLTRGAT YNIIVEALKD QQRHKVREEV VTVGNS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 6.5, Details 10 mM TRIS, 150 mM sodium chloride, 0.02 ug/mL TSP, 1 mM sodium azide, 0.35 mM [U-13C; U-15N] 15th Fibronectin III domain from human fibronectin, 0.5 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 bar, Temperature 298 K, pH 6.5, Details 10 mM [U-2H] TRIS, 0.35 mM [U-13C; U-15N] 15th Fibronectin III domain from human fibronectin, 150 mM sodium chloride, 1 mM sodium azide, 0.02 ug/mL TSP, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
9	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.2) mM
10	EDTA	natural abundance	0.5 (±0.2) mM
11	TRIS	[U-2H]	10 (±0.2) mM
12	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
13	sodium azide	natural abundance	1 (±0.2) mM
14	sodium chloride	natural abundance	150 (±0.2) mM
15	D2O	natural abundance	100 mM

LACS Plot; CA

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

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5M0A, Strand ID: A Detail

Release date

2016-11-10

Citation

Solution structure of isolated 15th Fibronectin III domain from human fibronectin
Waltho, J.P., Cliff, M.J., Blumson, E., Humphries, M.

Related entities 1. Fibronectin, : 1 : 2 : 25 entities Detail

Interaction partners 1. Fibronectin, : 91 interactors Detail

More details for 91 interactors identified by 47 citations

Experiments performed 15 experiments Detail

1 3D HNCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 298 K, pH 6.5, Details 10 mM TRIS, 150 mM sodium chloride, 0.02 ug/mL TSP, 1 mM sodium azide, 0.35 mM [U-13C; U-15N] 15th Fibronectin III domain from human fibronectin, 0.5 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 3D HNCOCA

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 3d hncocacb

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

5 3d HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

6 3D HNCACO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

7 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 950 MHz at MRC Crick

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 298 K, pH 6.5, Details 10 mM [U-2H] TRIS, 0.35 mM [U-13C; U-15N] 15th Fibronectin III domain from human fibronectin, 150 mM sodium chloride, 1 mM sodium azide, 0.02 ug/mL TSP, 0.5 mM EDTA, 100% D2O

#	Name	Isotope labeling	Concentration
9	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.2) mM
10	EDTA	natural abundance	0.5 (±0.2) mM
11	TRIS	[U-2H]	10 (±0.2) mM
12	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
13	sodium azide	natural abundance	1 (±0.2) mM
14	sodium chloride	natural abundance	150 (±0.2) mM
15	D2O	natural abundance	100 mM

9 2D 1H-13C trosy aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.2) mM
10	EDTA	natural abundance	0.5 (±0.2) mM
11	TRIS	[U-2H]	10 (±0.2) mM
12	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
13	sodium azide	natural abundance	1 (±0.2) mM
14	sodium chloride	natural abundance	150 (±0.2) mM
15	D2O	natural abundance	100 mM

10 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 950 MHz at MRC Crick

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 950 MHz at MRC Crick

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

12 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.2) mM
10	EDTA	natural abundance	0.5 (±0.2) mM
11	TRIS	[U-2H]	10 (±0.2) mM
12	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
13	sodium azide	natural abundance	1 (±0.2) mM
14	sodium chloride	natural abundance	150 (±0.2) mM
15	D2O	natural abundance	100 mM

13 3D 1H-15N TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.02) mM
2	EDTA	natural abundance	0.5 (±0.02) mM
3	TRIS	natural abundance	10 (±0.2) mM
4	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
5	sodium azide	natural abundance	1 (±0.02) mM
6	sodium chloride	natural abundance	150 (±0.2) mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

14 3D 1H-13C TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.2) mM
10	EDTA	natural abundance	0.5 (±0.2) mM
11	TRIS	[U-2H]	10 (±0.2) mM
12	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
13	sodium azide	natural abundance	1 (±0.2) mM
14	sodium chloride	natural abundance	150 (±0.2) mM
15	D2O	natural abundance	100 mM

15 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
9	15th Fibronectin III domain from human fibronectin	[U-13C; U-15N]	0.35 (±0.2) mM
10	EDTA	natural abundance	0.5 (±0.2) mM
11	TRIS	[U-2H]	10 (±0.2) mM
12	TSP	natural abundance	0.00002 (±2.0E-7) mg/mL
13	sodium azide	natural abundance	1 (±0.2) mM
14	sodium chloride	natural abundance	150 (±0.2) mM
15	D2O	natural abundance	100 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34048_5m0a.nef
Input source #2: Coordindates	5m0a.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---400-------410-------420-------430-------440-------450-------460-------470-------480
NASTGQEALSQTTISWAPFQDTSEYIISCHPVGTDEEPLQFRVPGTSTSATLTGLTRGATYNIIVEALKDQQRHKVREEVVTVGNS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NASTGQEALSQTTISWAPFQDTSEYIISCHPVGTDEEPLQFRVPGTSTSATLTGLTRGATYNIIVEALKDQQRHKVREEVVTVGNS
--------10--------20--------30--------40--------50--------60--------70--------80------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	86	0	0	100.0

Content subtype: combined_34048_5m0a.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	850		100.0 (chain: A, length: 86)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4853 (1)	noe	100.0 (chain: A, length: 86)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	6 (1)	hbond	2.3 (chain: A, length: 86)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	146 (146)	.	96.5 (chain: A, length: 86)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 480
  - ¹³C chemical shifts: 280
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
416	THR	HG1	4.89
419	TYR	HH	10.8
422	SER	HG	5.42
440	THR	HG1	4.92
454	THR	HG1	5.08

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	485	474	97.7
¹³C chemical shifts	370	280	75.7
¹⁵N chemical shifts	96	90	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	174	173	99.4
¹³C chemical shifts	172	86	50.0
¹⁵N chemical shifts	82	82	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	311	301	96.8
¹³C chemical shifts	198	194	98.0
¹⁵N chemical shifts	14	8	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	52	100.0
¹³C chemical shifts	52	52	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	26	92.9
¹³C chemical shifts	27	23	85.2
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 100.0%
- Total number of restraints: 4775
- Weight of restraints: 1.0 (4775)
- Potential type of restraints: square-well-parabolic (4775)
- Range of distance target values: 2.05, 6.45 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 2.3%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 2.62, 2.62 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 86, Sequence coverage: 96.5%
- Total number of restraints: 146
- Total number of restraints per polymer type: 146
- Weight of restraints: 1.0 (146)
- Potential type of restraints: square-well-parabolic (146)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Fibronectin III domain, beta sheet protein, cell adhesion, inflammation, integrin binding

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Found 1 Document (2.42 seconds)

BMRB: 34048

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Fibronectin, : 1 : 2 : 25 entities Detail

Interaction partners 1. Fibronectin, : 91 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail