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BMRB: 25177

2MTQ

Solution Structure of a De Novo Designed Peptide that Sequesters Toxic Heavy Metals

Authors

Plegaria, J.S., Zuiderweg, E.R.P., Stemmler, T.L., Pecoraro, V.L.

Assembly

De Novo Designed Peptide that Sequesters Toxic Heavy Metals

Entity

1. De Novo Designed Peptide that Sequesters Toxic Heavy Metals (polymer, Thiol state: all free), 73 monomers, 8077.986 Da Detail

MGSWAEFKQR LAAIKTRCQA LGGSEAECAA FEKEIAAFES ELQAYKGKGN PEVEALRKEA AAIRDECQAY RHN

Formula weight

8077.986 Da

Source organism

Escherichia coli BL21(DE3)

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 91.2 %, Completeness (bb): 96.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.2 % (755 of 828)	89.4 % (388 of 434)	94.6 % (298 of 315)	87.3 % (69 of 79)
Backbone	96.1 % (419 of 436)	94.7 % (142 of 150)	97.7 % (209 of 214)	94.4 % (68 of 72)
Sidechain	87.6 % (403 of 460)	86.6 % (246 of 284)	92.3 % (156 of 169)	14.3 % (1 of 7)
Aromatic	77.4 % (48 of 62)	83.9 % (26 of 31)	70.0 % (21 of 30)	100.0 % (1 of 1)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. entity

MGSWAEFKQR LAAIKTRCQA LGGSEAECAA FEKEIAAFES ELQAYKGKGN PEVEALRKEA AAIRDECQAY RHN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		100 mM
9	sodium azide	natural abundance		0.5 %
10	PMSF	natural abundance		0.05 mM
11	TCEP	natural abundance		0.8 mM
12	entity	[U-100% 13C; U-100% 15N]		1 mM
13	D2O	natural abundance		100 %

Protein Blocks Logo

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

Release date

2016-09-27

Citation

Apoprotein Structure and Metal Binding Characterization of a de Novo Designed Peptide, α3DIV, that Sequesters Toxic Heavy Metals
Plegaria, J.S., Zuiderweg, E.R.P., Stemmler, T.L., Pecoraro, V.L.
Biochemistry (2015), 54, 2858-2873, PubMed 25790102 , DOI 10.1021/acs.biochem.5b00064 , Abstract

Related entities 1. De Novo Designed Peptide that Sequesters Toxic Heavy Metals, : 1 : 1 : 6 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HN(CO)CA

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNHA

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D HCCH-COSY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 2D 1H-13C HSQC

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		100 mM
2	sodium azide	natural abundance		0.5 %
3	PMSF	natural abundance		0.05 mM
4	TCEP	natural abundance		0.8 mM
5	entity	[U-100% 13C; U-100% 15N]		1 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		100 mM
9	sodium azide	natural abundance		0.5 %
10	PMSF	natural abundance		0.05 mM
11	TCEP	natural abundance		0.8 mM
12	entity	[U-100% 13C; U-100% 15N]		1 mM
13	D2O	natural abundance		100 %

12 3D 1H-13C NOESY aromatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		100 mM
9	sodium azide	natural abundance		0.5 %
10	PMSF	natural abundance		0.05 mM
11	TCEP	natural abundance		0.8 mM
12	entity	[U-100% 13C; U-100% 15N]		1 mM
13	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25177_2mtq.nef
Input source #2: Coordindates	2mtq.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---
MGSWAEFKQRLAAIKTRCQALGGSEAECAAFEKEIAAFESELQAYKGKGNPEVEALRKEAAAIRDECQAYRHN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSWAEFKQRLAAIKTRCQALGGSEAECAAFEKEIAAFESELQAYKGKGNPEVEALRKEAAAIRDECQAYRHN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0

Content subtype: combined_25177_2mtq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	760		97.3 (chain: A, length: 73)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1866 (1)	noe	94.5 (chain: A, length: 73)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	78 (1)	hbond	69.9 (chain: A, length: 73)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	136 (133)	.	89.0 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 393
  - ¹³C chemical shifts: 298
  - ¹⁵N chemical shifts: 69
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 94.5%
- Total number of restraints: 1866
- Weight of restraints: 1.0 (1866)
- Potential type of restraints: upper-bound-parabolic (1866)
- Range of distance target values: 3.0, 7.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 69.9%
  - Total number of restraints: 78
  - Weight of restraints: 1.0 (78)
  - Potential type of restraints: upper-bound-parabolic (78)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 89.0%
- Total number of restraints: 133
- Total number of restraints per polymer type: 133
- Weight of restraints: 1.0 (133)
- Potential type of restraints: square-well-parabolic (133)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords De Novo Protein Design, Three-helix bundle, Triscysteine