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BMRB: 15946

2K76

Solution structure of a paralog-specific Mena binder by NMR

Authors

Link, N.M., Hunke, C., Eichler, J., Bayer, P.

Assembly

pGolemi

Entity

1. pGolemi (polymer, Thiol state: not present), 30 monomers, 3458.820 Da Detail

PFPPTPPGEE APVEDLIRFY NDLQQYLNVV

Formula weight

3458.82 Da

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.5 %, Completeness (bb): 92.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	88.5 % (170 of 192)	88.5 % (170 of 192)
Backbone	92.7 % (51 of 55)	92.7 % (51 of 55)
Sidechain	86.9 % (119 of 137)	86.9 % (119 of 137)
Aromatic	88.9 % (16 of 18)	88.9 % (16 of 18)
Methyl	100.0 % (16 of 16)	100.0 % (16 of 16)

1. pGolemi

PFPPTPPGEE APVEDLIRFY NDLQQYLNVV

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 45mM phosphate buffer NA

#	Name	Isotope labeling	Concentration
1	pGolemi	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	phosphate buffer	natural abundance	45 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2K76, Strand ID: A Detail

Release date

2009-04-03

Citation 1

The solution structure of pGolemi, a high affinity Mena EVH1 binding miniature protein, suggests explanations for paralog-specific binding to Ena/VASP homology (EVH) 1 domains
Link, N.M., Hunke, C., Mueller, J.W., Eichler, J., Bayer, P.
Biol. Chem. (2009), 390, 417-426, PubMed 19284291 , DOI 10.1515/BC.2009.045 , Abstract

Show more 2 citaions

Citation 2

High affinity, paralog-specific recognition of the Mena EVH1 domain by a miniature protein
Golemi-Kotra, D., Mahaffy, R., Footer, M.J., Holtzman, J.H., Pollard, T.D., Theriot, J.A., Schepartz, A.
J. Am. Chem. Soc. (2004), 126, 4-5, PubMed 14709031 , DOI 10.1021/ja037954k , Abstract

Citation 3

Miniature protein ligands for EVH1 domains: interplay between affinity, specificity, and cell motility
Holtzman, J.H., Woronowicz, K., Golemi-Kotra, D., Schepartz, A.
Biochemistry (2007), 46, 13541-13553, PubMed 17973491 , DOI 10.1021/bi700975f , Abstract

Hide non-primary 2 citaions

Related entities 1. pGolemi, : 1 : 106 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_15946_2k76.nef
Input source #2: Coordindates	2k76.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
PFPPTPPGEEAPVEDLIRFYNDLQQYLNVV
||||||||||||||||||||||||||||||
PFPPTPPGEEAPVEDLIRFYNDLQQYLNVV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	30	0	0	100.0

Content subtype: combined_15946_2k76.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	182		100.0 (chain: A, length: 30)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	525 (1)	noe	100.0 (chain: A, length: 30)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	26 (1)	hbond	56.7 (chain: A, length: 30)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	49 (49)	.	100.0 (chain: A, length: 30)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 182
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	174	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	54	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	137	120	87.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	16	88.9

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 30, Sequence coverage: 100.0%
- Total number of restraints: 524
- Weight of restraints: 1.0 (524)
- Potential type of restraints: square-well-parabolic (524)
- Range of distance target values: 1.9, 6.9 (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: 30, Sequence coverage: 56.7%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: square-well-parabolic (26)
  - Range of distance target values: 1.85, 2.85 (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: 30, Sequence coverage: 100.0%
- Total number of restraints: 49
- Total number of restraints per polymer type: 49
- Weight of restraints: 1.0 (49)
- Potential type of restraints: square-well-parabolic (49)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Ligand Design, NMR spectroscopy, Peptides, Structure Elucidation, ActA homolog, aPP, beta-hairpin, miniature protein, protein design

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Found 1 Document (0.575 seconds)

BMRB: 15946

Sample

Related entities 1. pGolemi, : 1 : 106 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail