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BMRB: 16007

2KA0

NMR structure of the protein TM1367

Authors

Mohanty, B., Pedrini, B., Serrano, P., Geralt, M., Horst, R., Wilson, I., Wuthrich, K.

Assembly

TM1367

Entity

1. TM1367 (polymer, Thiol state: not present), 124 monomers, 13922.95 Da Detail

MRVELLFESG KCVIDLNEEY EVVKLLKEKI PFESVVNTWG EEIYFSTPVN VQKMENPREV VEIGDVGYWP PGKALCLFFG KTPMSDDKIQ PASAVNVIGK IVEGLEDLKK IKDGEKVAVR FASS

Formula weight

13922.95 Da

Source organism

Thermotoga maritima

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.2 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.2 % (1426 of 1483)	97.8 % (757 of 774)	93.7 % (546 of 583)	97.6 % (123 of 126)
Backbone	96.8 % (707 of 730)	98.0 % (245 of 250)	95.9 % (348 of 363)	97.4 % (114 of 117)
Sidechain	96.0 % (833 of 868)	97.7 % (512 of 524)	93.1 % (312 of 335)	100.0 % (9 of 9)
Aromatic	70.4 % (76 of 108)	81.5 % (44 of 54)	57.7 % (30 of 52)	100.0 % (2 of 2)
Methyl	100.0 % (148 of 148)	100.0 % (74 of 74)	100.0 % (74 of 74)

1. TM1367

MRVELLFESG KCVIDLNEEY EVVKLLKEKI PFESVVNTWG EEIYFSTPVN VQKMENPREV VEIGDVGYWP PGKALCLFFG KTPMSDDKIQ PASAVNVIGK IVEGLEDLKK IKDGEKVAVR FASS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

LACS Plot; CA

Referencing offset: -0.22 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.22 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.48 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KA0, Strand ID: A Detail

Release date

2009-04-13

Citation

Comparison of NMR and crystal structures for the proteins TM1112 and TM1367
Mohanty, B., Serrano, P., Pedrini, B., Jaudzems, K., Geralt, M., Horst, R., Herrmann, T., Elsliger, M., Wilson, I.A., Wuthrich, K.
Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. (2010), 66, 1381-1392, PubMed 20944235 , DOI 10.1107/S1744309110020956 , Abstract

Related entities 1. TM1367, : 1 : 1 : 1 entities Detail

Experiments performed 8 experiments Detail

1 2D [15N,1H] HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

2 2D [13C,1H] HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

3 3D 15N - resolved [1H,1H] NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

4 3D 13C-resolved [1H,1H] NOESY, aliphatic 13C

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

5 3D 13C-resolved [1H,1H] NOESY, aromatic 13C

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

6 4D-APSY-HACANH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

7 5D-APSY-HACACONH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

8 5D-APSY-CBCACONH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	DTT	natural abundance		0.5 mM
2	D10-DTT	natural abundance		4.5 mM
3	sodium azide	natural abundance		0.03 %
4	sodium chloride	natural abundance		50 mM
5	sodium phosphate	natural abundance		25 mM
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %
8	TM1367	[U-98% 13C; U-98% 15N]		1.5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16007_2ka0.nef
Input source #2: Coordindates	2ka0.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--------80--------90-------100
MRVELLFESGKCVIDLNEEYEVVKLLKEKIPFESVVNTWGEEIYFSTPVNVQKMENPREVVEIGDVGYWPPGKALCLFFGKTPMSDDKIQPASAVNVIGK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MRVELLFESGKCVIDLNEEYEVVKLLKEKIPFESVVNTWGEEIYFSTPVNVQKMENPREVVEIGDVGYWPPGKALCLFFGKTPMSDDKIQPASAVNVIGK

-------110-------120----
IVEGLEDLKKIKDGEKVAVRFASS
||||||||||||||||||||||||
IVEGLEDLKKIKDGEKVAVRFASS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	124	0	0	100.0

Content subtype: combined_16007_2ka0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1442		100.0 (chain: A, length: 124)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3411 (1)	noe	100.0 (chain: A, length: 124)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 766
  - ¹³C chemical shifts: 550
  - ¹⁵N chemical shifts: 126
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 124, Sequence coverage: 100.0%
- Total number of restraints: 3411
- Weight of restraints: 1.0 (3411)
- Potential type of restraints: upper-bound-parabolic (3411)
- Range of distance target values: 2.4, 5.5 (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

Keywords Thermotoga Maritima, TM1367