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BMRB: 34033

5LO4

Engineering protein stability with atomic precision in a monomeric miniprotein

Authors

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

Assembly

PPa-CH3

Entity

1. PPa-CH3 (polymer, Thiol state: not present), 36 monomers, 3795.317 Da Detail

XPPTKPTKPG DNATPEKLAK XQADLAKXQK DLADXX

Formula weight

3795.317 Da

Source organism

Streptococcus mutans

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.3 %, Completeness: 60.2 %, Completeness (bb): 56.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	60.2 % (213 of 354)	83.2 % (158 of 190)	20.0 % (27 of 135)	96.6 % (28 of 29)
Backbone	56.8 % (100 of 176)	94.8 % (55 of 58)	21.7 % (20 of 92)	96.2 % (25 of 26)
Sidechain	57.7 % (120 of 208)	78.0 % (103 of 132)	19.2 % (14 of 73)	100.0 % (3 of 3)
Methyl	67.9 % (19 of 28)	85.7 % (12 of 14)	50.0 % (7 of 14)

1. entity 1

XPPTKPTKPG DNATPEKLAK XQADLAKXQK DLADX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.4, Details 1 mM PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	natural abundance		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5LO4, 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. PPa-CH3, : 1 : 2 : 7 entities Detail

Experiments performed 8 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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	natural abundance		1 mM

8 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 PPa-CH3, 8.2 mM Na2HPO4, 1.8 mM KH2PO4, 137 mM NaCl, 13.7 mM NaOH, 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	PPa-CH3	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_34033_5lo4.nef
Input source #2: Coordindates	5lo4.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
1:20:LYS:C	1:21:4PH:N	unknown	unknown	n/a
1:21:4PH:C	1:22:GLN:N	unknown	unknown	n/a
1:27:LYS:C	1:28:4PH:N	unknown	unknown	n/a
1:28:4PH:C	1:29:GLN:N	unknown	unknown	n/a
1:34:ASP:C	1:35:4PH:N	unknown	unknown	n/a
1:35:4PH: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	20	4PH	4-methyl-L-phenylalanine	Assigned chemical shifts, Distance restraints, Coordinates
A	27	4PH	4-methyl-L-phenylalanine	Assigned chemical shifts, Distance restraints, Coordinates
A	34	4PH	4-methyl-L-phenylalanine	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-----
XPPTKPTKPGDNATPEKLAKXQADLAKXQKDLADXX
||||||||||||||||||||||||||||||||||||
XPPTKPTKPGDNATPEKLAKXQADLAKXQKDLADXX
--------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_34033_5lo4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	7		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	261		97.2 (chain: A, length: 36)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	444 (1)	noe	91.7 (chain: A, length: 36)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	40 (40)	.	83.3 (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: 191
  - ¹³C chemical shifts: 38
  - ¹⁵N chemical shifts: 32
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 36, Sequence coverage: 91.7%
- Total number of restraints: 442
- Weight of restraints: 1.0 (442)
- Potential type of restraints: square-well-parabolic (442)
- Range of distance target values: 1.54, 5.07 (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: 83.3%
- Total number of restraints: 40
- Total number of restraints per polymer type: 40
- Weight of restraints: 1.0 (40)
- Potential type of restraints: square-well-parabolic (40)
- 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