BMRBj - BMREntryMaster

Found 1 Document (0.732 seconds)

BMRB: 15879

2K6R

Protein folding on a highly rugged landscape: Experimental observation of glassy dynamics and structural frustration

Authors

Sadqi, M., de Alba, E., Perez-Jimenez, R., Sanchez-Ruiz, J.M., Munoz, V.

Assembly

FSD mod

Entity

1. FSD mod (polymer, Thiol state: not present), 29 monomers, 3847.363 Da Detail

GQQYTAXIKG RTFRNEKELR DFIEKFXGR

Formula weight

3847.363 Da

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.7 %, Completeness: 60.8 %, Completeness (bb): 57.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	60.8 % (192 of 316)	90.3 % (168 of 186)	18.5 % (24 of 130)
Backbone	57.0 % (77 of 135)	93.0 % (53 of 57)	30.8 % (24 of 78)
Sidechain	56.6 % (116 of 205)	89.1 % (115 of 129)	1.3 % (1 of 76)
Aromatic	44.7 % (17 of 38)	89.5 % (17 of 19)	0.0 % (0 of 19)
Methyl	50.0 % (9 of 18)	100.0 % (9 of 9)	0.0 % (0 of 9)

1. FSD mod

GQQYTAXIKG RTFRNEKELR DFIEKFXGR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	FSD_mod	natural abundance	1 mM
2	DSS	natural abundance	0.05 mM
3	D2O	[U-99.9% 2H]	10 %
4	H2O	natural abundance	90 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2K6R, Strand ID: A Detail

Release date

2009-03-11

Citation

A designed protein as experimental model of primordial folding
Sadqi, M., de Alba, E., Perez-Jimenez, R., Sanchez-Ruiz, J.M., Munoz, V.
Proc. Natl. Acad. Sci. U. S. A. (2009), 106, 4127-4132, PubMed 19240216 , DOI 10.1073/pnas.0812108106 , Abstract

Related entities 1. FSD mod, : 1 : 2 : 4 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15879_2k6r.nef
Input source #2: Coordindates	2k6r.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:6:ALA:C	1:7:NAL:N	unknown	unknown	n/a
1:26:PHE:C	1:27:DNS:N	unknown	unknown	n/a
1:27:DNS:C	1:28:GLY:N	unknown	unknown	n/a
1:7:NAL:C	1:8:ILE:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	7	NAL	BETA-(2-NAPHTHYL)-ALANINE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	27	DNS	N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20---------
GQQYTAXIKGRTFRNEKELRDFIEKFXGR
|||||||||||||||||||||||||||||
GQQYTAXIKGRTFRNEKELRDFIEKFXGR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	29	0	0	100.0

Content subtype: combined_15879_2k6r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	217		96.6 (chain: A, length: 29)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	674 (1)	noe	89.7 (chain: A, length: 29)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	14 (1)	hbond	37.9 (chain: A, length: 29)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	46 (46)	.	89.7 (chain: A, length: 29)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 96.6%
- Total number of assignments
  - ¹H chemical shifts: 194
  - ¹³C chemical shifts: 23
- 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

Comp_index_ID	Comp_ID
7	NAL
27	DNS

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	186	168	90.3
¹³C chemical shifts	130	21	16.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	53	93.0
¹³C chemical shifts	54	21	38.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	129	115	89.1
¹³C chemical shifts	76	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0
¹³C chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	17	89.5
¹³C chemical shifts	19	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 89.7%
- Total number of restraints: 626
- Weight of restraints: 1.0 (626)
- Potential type of restraints: square-well-parabolic (626)
- Range of distance target values: 2.15, 4.0 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 29, Sequence coverage: 37.9%
  - Total number of restraints: 14
  - Weight of restraints: 1.0 (14)
  - Potential type of restraints: square-well-parabolic (14)
  - Range of distance target values: 2.2, 3.1 (Å)
  - Histogram of distance target values
  - 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: 29, Sequence coverage: 89.7%
- Total number of restraints: 46
- Total number of restraints per polymer type: 46
- Weight of restraints: 1.0 (46)
- Potential type of restraints: square-well-parabolic (46)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords de novo protein design, non-natural amino acids, rugged folding energy landscape, structural frustration, synthetic protein

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Found 1 Document (0.732 seconds)

BMRB: 15879

Sample

Related entities 1. FSD mod, : 1 : 2 : 4 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail