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BMRB: 34031

5LO2

Engineering protein stability with atomic precision in a monomeric miniprotein

Authors

Baker, E.G., Hudson, K.L., Williams, C., Bartlett, G.G., Heal, J.W., Sessions, R.B., Crump, M.P., Woolfson, D.N.

Assembly

PPaTyr

Entity

1. PPaTyr (polymer, Thiol state: not present), 36 monomers, 3801.236 Da Detail

XPPTKPTKPG DNATPEKLAK YQADLAKYQK DLADYX

Formula weight

3801.236 Da

Source organism

Streptococcus mutans

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 66.7 %, Completeness (bb): 58.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	66.7 % (268 of 402)	88.3 % (189 of 214)	30.1 % (47 of 156)	100.0 % (32 of 32)
Backbone	58.8 % (114 of 194)	96.9 % (62 of 64)	22.8 % (23 of 101)	100.0 % (29 of 29)
Sidechain	66.0 % (159 of 241)	84.7 % (127 of 150)	33.0 % (29 of 88)	100.0 % (3 of 3)
Aromatic	100.0 % (24 of 24)	100.0 % (12 of 12)	100.0 % (12 of 12)
Methyl	67.9 % (19 of 28)	100.0 % (14 of 14)	35.7 % (5 of 14)

1. entity 1

XPPTKPTKPG DNATPEKLAK YQADLAKYQK DLADYX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5LO2, Strand ID: A Detail

Release date

2017-05-07

Citation

Engineering protein stability with atomic precision in a monomeric miniprotein
Baker, E.G., Williams, C., Hudson, K.L., Bartlett, G.G., Heal, J.W., Porter Goff, K.L., Sessions, R.B., Crump, M.P., Woolfson, D.N.
Nat. Chem. Biol. (2017), 13, 764-770, PubMed 28530710 , DOI 10.1038/nchembio.2380 , Abstract

Related entities 1. PPaTyr, : 1 : 2 : 22 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz microcryoprobe-equipped

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

2 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz microcryoprobe-equipped

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

3 2D 1H-1H TOCSY

Instrument

Bruker AvanceIII - 700 MHz microcryoprobe-equipped

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

4 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz microcryoprobe-equipped

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

5 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 700 MHz microcryoprobe-equipped

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

6 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 900 MHz TCI 5mm z-PFG cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

7 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 900 MHz TCI 5mm z-PFG cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

8 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 900 MHz TCI 5mm z-PFG cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

9 2D DQF-COSY

Instrument

Bruker AvanceIII - 900 MHz TCI 5mm z-PFG cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM NA PPalphaTyr, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	KH2PO4	natural abundance		1.8 mM
2	Na2HPO4	natural abundance		8.2 mM
3	NaCl	natural abundance		137 mM
4	NaOH	natural abundance		13.7 mM
5	PPalphaTyr	natural abundance		1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34031_5lo2.nef
Input source #2: Coordindates	5lo2.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)
1:1:ACE:C	1:2:PRO:N	unknown	unknown	n/a
1:35:TYR:C	1:36:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	ACE	ACETYL GROUP	Assigned chemical shifts, Coordinates
A	35	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

0--------10--------20--------30-----
XPPTKPTKPGDNATPEKLAKYQADLAKYQKDLADYX
||||||||||||||||||||||||||||||||||||
XPPTKPTKPGDNATPEKLAKYQADLAKYQKDLADYX
--------10--------20--------30------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	36	0	0	100.0

Content subtype: combined_34031_5lo2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	262		97.2 (chain: A, length: 36)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	617 (1)	noe	94.4 (chain: A, length: 36)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	43 (43)	.	72.2 (chain: A, length: 36)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 188
  - ¹³C chemical shifts: 42
  - ¹⁵N chemical shifts: 32
- 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

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: 36, Sequence coverage: 94.4%
- Total number of restraints: 604
- Weight of restraints: 1.0 (604)
- Potential type of restraints: square-well-parabolic (604)
- Range of distance target values: 1.58, 5.0 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 72.2%
- Total number of restraints: 43
- Total number of restraints per polymer type: 43
- Weight of restraints: 1.0 (43)
- Potential type of restraints: square-well-parabolic (43)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Designed miniprotein CH-pi weak non-covalent interactions in protiens solution structure proline-tyrosine interactions, STRUCTURAL PROTEIN