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BMRB: 15478

2JVF

1H and 15N resonance assignment of M7, a computationally-designed artificial protein

Authors

Stordeur, C., Dalluege, R., Birkenmeier, O., Wienk, H., Rudolph, R., Lange, C., Luecke, C.

Assembly

M7

Entity

1. M7 (polymer, Thiol state: not present), 96 monomers, 10820.31 Da Detail

GSHMKVDITI KIQRDGQEIE IDIRVSTGKE LERALQELEK ALARAGARNV QITISAENDE QAKELLELIA RLLQKLGYKD INVRVNGTEV KIEVRV

Formula weight

10820.31 Da

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 97.9 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	97.9 % (685 of 700)	98.0 % (582 of 594)	97.2 % (103 of 106)
Backbone	96.3 % (283 of 294)	96.0 % (190 of 198)	96.9 % (93 of 96)
Sidechain	99.0 % (402 of 406)	99.0 % (392 of 396)	100.0 % (10 of 10)
Aromatic	100.0 % (6 of 6)	100.0 % (6 of 6)
Methyl	100.0 % (70 of 70)	100.0 % (70 of 70)

1. M7

GSHMKVDITI KIQRDGQEIE IDIRVSTGKE LERALQELEK ALARAGARNV QITISAENDE QAKELLELIA RLLQKLGYKD INVRVNGTEV KIEVRV

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	M7	natural abundance		1.0 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium azide	natural abundance		0.05 %
4	H2O			95 %
5	D2O			5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	M7	[U-98% 15N]		1.3 mM
7	sodium phosphate	natural abundance		25 mM
8	sodium azide	natural abundance		0.05 %
9	H2O			95 %
10	D2O			5 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
11	M7	natural abundance		1.0 mM
12	sodium phosphate	natural abundance		25 mM
13	sodium azide	natural abundance		0.05 %
14	D2O			100 %

Protein Blocks Logo

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

Release date

2008-06-24

Citation 1

The NMR solution structure of the artificial protein M7 matches the computationally designed model
Stordeur, C., Dalluege, R., Birkenmeier, O., Wienk, H., Rudolph, R., Lange, C., Luecke, C.
Proteins (2008), 72, 1104-1107, PubMed 18498106 , DOI 10.1002/prot.22107 , Abstract

Show more 1 citaion

Citation 2

A tetrapeptide fragment-based design method results in highly stable artificial proteins
Dalluege, R., Oschmann, J., Birkenmeier, O., Luecke, C., Lilie, H., Rudolph, R., Lange, C.
Proteins (2007), 68, 839-849, PubMed 17557327 , DOI 10.1002/prot.21493 , Abstract

Hide non-primary 1 citaion

Related entities 1. M7, : 1 : 9 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	M7	natural abundance		1.0 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium azide	natural abundance		0.05 %
4	H2O			95 %
5	D2O			5 %

2 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	M7	natural abundance		1.0 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium azide	natural abundance		0.05 %
4	H2O			95 %
5	D2O			5 %

3 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	M7	[U-98% 15N]		1.3 mM
7	sodium phosphate	natural abundance		25 mM
8	sodium azide	natural abundance		0.05 %
9	H2O			95 %
10	D2O			5 %

4 3D 1H-15N TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	M7	[U-98% 15N]		1.3 mM
7	sodium phosphate	natural abundance		25 mM
8	sodium azide	natural abundance		0.05 %
9	H2O			95 %
10	D2O			5 %

5 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	M7	[U-98% 15N]		1.3 mM
7	sodium phosphate	natural abundance		25 mM
8	sodium azide	natural abundance		0.05 %
9	H2O			95 %
10	D2O			5 %

6 2D 1H-15N HTQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	M7	[U-98% 15N]		1.3 mM
7	sodium phosphate	natural abundance		25 mM
8	sodium azide	natural abundance		0.05 %
9	H2O			95 %
10	D2O			5 %

7 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
11	M7	natural abundance		1.0 mM
12	sodium phosphate	natural abundance		25 mM
13	sodium azide	natural abundance		0.05 %
14	D2O			100 %

8 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
11	M7	natural abundance		1.0 mM
12	sodium phosphate	natural abundance		25 mM
13	sodium azide	natural abundance		0.05 %
14	D2O			100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15478_2jvf.nef
Input source #2: Coordindates	2jvf.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

------------10--------20--------30--------40--------50--------60--------70--------80--------90--
GSHMKVDITIKIQRDGQEIEIDIRVSTGKELERALQELEKALARAGARNVQITISAENDEQAKELLELIARLLQKLGYKDINVRVNGTEVKIEVRV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMKVDITIKIQRDGQEIEIDIRVSTGKELERALQELEKALARAGARNVQITISAENDEQAKELLELIARLLQKLGYKDINVRVNGTEVKIEVRV
--------10--------20--------30--------40--------50--------60--------70--------80--------90------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_15478_2jvf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	699		97.9 (chain: A, length: 96)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1279 (1)	noe	96.9 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 97.9%
- Total number of assignments
  - ¹H chemical shifts: 588
  - ¹⁵N chemical shifts: 111
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 96.9%
- Total number of restraints: 1270
- Weight of restraints: 1.0 (1270)
- Potential type of restraints: upper-bound-parabolic (1270)
- Range of distance target values: 2.5, 10.4 (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

Keywords artificial fold, de novo protein, tetrapeptide fragment-based protein design