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BMRB: 30088

5JXV

Solid-state MAS NMR structure of beta 1 domain of protein G (GB1)

Authors

Andreas, L.B., Jaudzems, K., Stanek, J., Lalli, D., Bertarello, A., Le Marchand, T., Cala-De Paepe, D., Kotelovica, S., Akopjana, I., Knott, B., Wegner, S., Engelke, F., Lesage, A., Emsley, L., Tars, K., Herrmann, T., Pintacuda, G.

Assembly

Immunoglobulin G-binding protein G

Entity

1. Immunoglobulin G-binding protein G (polymer, Thiol state: not present), 56 monomers, 6222.757 Da Detail

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTE

Formula weight

6222.757 Da

Source organism

Streptococcus dysgalactiae subsp. equisimilis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.4 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.4 % (577 of 631)	90.7 % (291 of 321)	90.3 % (224 of 248)	100.0 % (62 of 62)
Backbone	98.8 % (332 of 336)	97.4 % (113 of 116)	99.4 % (163 of 164)	100.0 % (56 of 56)
Sidechain	85.3 % (296 of 347)	86.8 % (178 of 205)	82.4 % (112 of 136)	100.0 % (6 of 6)
Aromatic	21.4 % (12 of 56)	21.4 % (6 of 28)	18.5 % (5 of 27)	100.0 % (1 of 1)
Methyl	100.0 % (64 of 64)	100.0 % (32 of 32)	100.0 % (32 of 32)

1. Immunoglobulin G-binding protein G

MQYKLILNGK TLKGETTTEA VDAATAEKVF KQYANDNGVD GEWTYDDATK TFTVTE

Show sample condition

Sample

Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.27 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.0 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2016-08-07

Citation

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR
Andreas, L.B., Jaudzems, K., Stanek, J., Lalli, D., Bertarello, A., Marchand, T.LE., Paepe, D.CD., Kotelovica, S., Akopjana, I., Knott, B., Wegner, S., Engelke, F., Lesage, A., Emsley, L., Tars, K., Herrmann, T., Pintacuda, G.
Proc. Natl. Acad. Sci. U. S. A. (2016), 113, 9187-9192, PubMed 27489348 , DOI 10.1073/pnas.1602248113 , Abstract

Related entities 1. Immunoglobulin G-binding protein G, : 1 : 20 : 2 : 47 : 38 entities Detail

Interaction partners 1. Immunoglobulin G-binding protein G, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 (H)NCAH

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

2 (H)CANH

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

3 (H)(CO)CA(CO)NH

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

4 (H)(CA)CB(CA)NH

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

5 (H)N(CA)(CO)NH

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

6 (H)N(CO)(CA)NH

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

7 (H)CCH-TOCSY

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

8 (H)NHH-RFDR

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

9 (H)CHH-RFDR

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

10 H(H)CH-RFDR-aromatic13C

Instrument

Bruker AvanceIII - na MHz MAS 111 kHz

Sample

State isotropic, Solvent system H20/MPD/IPA, Temperature 283 (±5) K, pH 5.6 (±0.1), Details 12.5 mM sodium phosphate, 45 % methyl-2,4-pentane diol, 22.5 % isopropyl alcohol, 800 mg/mL [U-99% 13C; U-99% 15N] B1 domain of Immunoglobulin G-Binding protein G, H20/MPD/IPA

#	Name	Isotope labeling	Type	Concentration
1	B1 domain of Immunoglobulin G-Binding protein G	[U-99% 13C; U-99% 15N]		800 (±300.0) mg/mL
2	isopropyl alcohol	natural abundance		22.5 (±5.0) %
3	methyl-2,4-pentane diol	natural abundance		45 (±5.0) %
4	sodium phosphate	natural abundance		12.5 (±5.0) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30088_5jxv.nef
Input source #2: Coordindates	5jxv.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------
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_30088_5jxv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	583		100.0 (chain: A, length: 56)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	851 (1)	noe	100.0 (chain: A, length: 56)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	108 (108)	.	100.0 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 294
  - ¹³C chemical shifts: 224
  - ¹⁵N chemical shifts: 65
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of restraints: 849
- Weight of restraints: 1.0 (849)
- Potential type of restraints: upper-bound-parabolic (849)
- Range of distance target values: 2.96, 5.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of restraints: 108
- Total number of restraints per polymer type: 108
- Weight of restraints: 1.0 (108)
- Potential type of restraints: square-well-parabolic (108)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Globular, alpha beta, immune system