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BMRB: 30573

6O0C

NMR ensemble of computationally designed protein XAA_GVDQ mutant M4L

Authors

Wei, K.Y., Moschidi, D., Nerli, S., Sgourakis, N., Baker, D.

Assembly

Design construct XAA GVDQ mutant M4L

Entity

1. Design construct XAA GVDQ mutant M4L (polymer, Thiol state: not present), 96 monomers, 10957.40 × 3 Da Detail

GSHLGDLKYS LERLREILER LEENPSEKQI VEAIRAIVEN NAQIVEAIRA IVENNAQIVE NNRAIIEALE AIGVDQKILE EMKKQLKDLK RSLERG

Total weight

32872.203 Da

Max. entity weight

10957.4 Da

Source organism

synthetic construct

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.8 %, Completeness: 52.0 %, Completeness (bb): 81.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.0 % (596 of 1146)	31.7 % (192 of 606)	72.3 % (313 of 433)	85.0 % (91 of 107)
Backbone	81.9 % (470 of 574)	54.9 % (107 of 195)	95.8 % (272 of 284)	95.8 % (91 of 95)
Sidechain	32.4 % (215 of 664)	20.7 % (85 of 411)	53.9 % (130 of 241)	0.0 % (0 of 12)
Aromatic	0.0 % (0 of 12)	0.0 % (0 of 6)	0.0 % (0 of 6)
Methyl	63.4 % (85 of 134)	64.2 % (43 of 67)	62.7 % (42 of 67)

1. entity 1

GSHLGDLKYS LERLREILER LEENPSEKQI VEAIRAIVEN NAQIVEAIRA IVENNAQIVE NNRAIIEALE AIGVDQKILE EMKKQLKDLK RSLERG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 600 uM U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val k170_MAI(LV)proS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	k170_MAI(LV)proS	U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val		600 uM
2	NaCl	natural abundance		100 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 400 uM U-[15N, 13C, 2H] k170_ILVstar, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	k170_ILVstar	U-[15N, 13C, 2H]		400 uM
4	NaCl	natural abundance		100 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 6O0C, Strand ID: A, B, C Detail

Release date

2019-03-21

Citation

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds
Wei, K.Y., Moschidi, D., Bick, M.J., Nerli, S., McShan, A.C., Carter, L.P., Huang, P.S., Fletcher, D.A., Sgourakis, N.G., Boyken, S.E., Baker, D.
Proc. Natl. Acad. Sci. U. S. A. (2020), 117, 7208-7215, PubMed 32188784 , DOI 10.1073/pnas.1914808117 , Abstract

Related entities 1. Design construct XAA GVDQ mutant M4L, : 1 : 2 : 34 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-13C HSQC

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 600 uM U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val k170_MAI(LV)proS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	k170_MAI(LV)proS	U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val		600 uM
2	NaCl	natural abundance		100 mM

2 3D CM-CMHM NOESY

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 600 uM U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val k170_MAI(LV)proS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	k170_MAI(LV)proS	U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val		600 uM
2	NaCl	natural abundance		100 mM

3 3D CM-NHN NOESY

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 600 uM U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val k170_MAI(LV)proS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	k170_MAI(LV)proS	U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val		600 uM
2	NaCl	natural abundance		100 mM

4 3D HNHa-CMHM NOESY

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 600 uM U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val k170_MAI(LV)proS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	k170_MAI(LV)proS	U-[15N, 12C, 2H] 13Ce Met 13Cb Ala 13Cd1 Ile 13Cd2 Leu 13Cg2 Val		600 uM
2	NaCl	natural abundance		100 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 400 uM U-[15N, 13C, 2H] k170_ILVstar, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	k170_ILVstar	U-[15N, 13C, 2H]		400 uM
4	NaCl	natural abundance		100 mM

6 3D HNCO

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 400 uM U-[15N, 13C, 2H] k170_ILVstar, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	k170_ILVstar	U-[15N, 13C, 2H]		400 uM
4	NaCl	natural abundance		100 mM

7 3D HNCACB

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 400 uM U-[15N, 13C, 2H] k170_ILVstar, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	k170_ILVstar	U-[15N, 13C, 2H]		400 uM
4	NaCl	natural abundance		100 mM

8 3D HNCA

Instrument

Bruker Avance III - 800 MHz TCI cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.2, Details 400 uM U-[15N, 13C, 2H] k170_ILVstar, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
3	k170_ILVstar	U-[15N, 13C, 2H]		400 uM
4	NaCl	natural abundance		100 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30573_3.str
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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30573_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	1761		95.8 (chain: 1, length: 96)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 96, Sequence coverage: 95.8%
- Total number of assignments
  - ¹H chemical shifts: 597
  - ¹³C chemical shifts: 891
  - ¹⁵N chemical shifts: 273
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords de novo protein