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BMRB: 25123

2MSG

13C,15N solid-state NMR chemical shift assignments for microcrystallized Ubiquitin in MPD

Authors

Fasshuber, H., Lakomek, N., Habenstein, B., Loquet, A., Shi, C., Giller, K., Wolff, S., Becker, S., Lange, A.

Assembly

microcrystallized Ubiquitin in MPD

Entity

1. microcrystallized Ubiquitin in MPD (polymer, Thiol state: not present), 72 monomers, 8181.284 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LR

Formula weight

8181.284 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 92.7 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	92.7 % (382 of 412)	93.7 % (314 of 335)	88.3 % (68 of 77)
Backbone	96.8 % (272 of 281)	96.2 % (204 of 212)	98.6 % (68 of 69)
Sidechain	88.4 % (176 of 199)	92.1 % (176 of 191)	0.0 % (0 of 8)
Aromatic	81.3 % (13 of 16)	81.3 % (13 of 16)
Methyl	95.7 % (45 of 47)	95.7 % (45 of 47)

1. Ubiquitin

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LR

LACS Plot; CA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MSG, Strand ID: A Detail

Release date

2015-10-13

Citation

Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR
Fasshuber, H., Lakomek, N., Habenstein, B., Loquet, A., Shi, C., Giller, K., Wolff, S., Becker, S., Lange, A.
Protein Sci. (2015), 24, 592-598, PubMed 25644665 , DOI 10.1002/pro.2654 , Abstract

Related entities 1. microcrystallized Ubiquitin in MPD, : 1 : 303 : 10 : 77 : 308 entities Detail

Interaction partners 1. microcrystallized Ubiquitin in MPD, : 27 interactors Detail

More details for 27 interactors identified by 16 citations

Experiments performed 15 experiments Detail

1 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

2 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

3 NCA

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

4 NCO

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

5 INEPT

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

6 NCACX

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

7 NCOCX

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

8 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

9 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

10 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

11 NCA

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

12 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

13 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

14 PDSD

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

15 NCA

Instrument

#1 Model Bruker Avance (800 MHz) Details standard bore

#2 Model Bruker Avance (850 MHz) Details wide bore

#3 Model Bruker Avance (600 MHz) Details wide bore

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25123_2msg.nef
Input source #2: Coordindates	2msg.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--
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	72	0	0	100.0

Content subtype: combined_25123_2msg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	408		98.6 (chain: A, length: 72)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	518 (1)	noe	83.3 (chain: A, length: 72)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 98.6%

--------10--------20--------30--------40--------50--------60--------70--
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 
--------10--------20--------30--------40--------50--------60--------70-

Total number of assignments
- ¹³C chemical shifts: 337
- ¹⁵N chemical shifts: 71

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	GLN	CD	180.089
4	PHE	CG	139.156
16	GLU	CD	178.661
18	GLU	CD	185.392
19	PRO	N	133.711
21	ASP	CG	181.457
24	GLU	CD	183.95
25	ASN	CG	174.216
31	GLN	CD	180.024
32	ASP	CG	178.783
37	PRO	N	142.589
38	PRO	N	136.594
39	ASP	CG	180.294
40	GLN	CD	179.22
45	PHE	CG	137.056
49	GLN	CD	178.924
52	ASP	CG	181.214
58	ASP	CG	180.61
59	TYR	CG	130.778
59	TYR	CZ	156.921
60	ASN	CG	178.083
62	GLN	CD	180.785
64	GLU	CD	183.865

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	335	317	94.6
¹⁵N chemical shifts	80	68	85.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	144	140	97.2
¹⁵N chemical shifts	69	68	98.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	191	177	92.7
¹⁵N chemical shifts	11	0	0.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	48	46	95.8

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	16	13	81.2

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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 83.3%
- Total number of restraints: 518
- Weight of restraints: 1.0 (518)
- Potential type of restraints: square-well-parabolic (518)
- Range of distance target values: 4.0, 4.0 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Protein