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BMRB: 36264

6K8Q

Solution structure of the intermembrane space domain of the mitochondrial import protein Tim21 from S. cerevisiae

Authors

Bala, S., Shinya, S., Srivastava, A., Shimada, A., Kobayashi, N., Kojima, C., Tama, F., Miyashita, O., Kohda, D.

Assembly

Mitochondrial import inner membrane translocase subunit TIM21

Entity

1. Mitochondrial import inner membrane translocase subunit TIM21 (polymer, Thiol state: all free), 115 monomers, 13544.37 Da Detail

GSDTQLFNRA VSMVEKNKDI RSLLQCDDGI TGKERLKAYG ELITNDKWTR NRPIVSTKKL DKEGRTHHYM RFHVESKKKI ALVHLEAKES KQNYQPDFIN MYVDVPGEKR YYLIK

Formula weight

13544.37 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 88.6 %, Completeness (bb): 93.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.6 % (1263 of 1425)	87.5 % (656 of 750)	90.1 % (490 of 544)	89.3 % (117 of 131)
Backbone	93.9 % (642 of 684)	91.8 % (214 of 233)	94.4 % (320 of 339)	96.4 % (108 of 112)
Sidechain	84.5 % (718 of 850)	84.5 % (437 of 517)	86.6 % (272 of 314)	47.4 % (9 of 19)
Aromatic	71.7 % (76 of 106)	73.6 % (39 of 53)	69.2 % (36 of 52)	100.0 % (1 of 1)
Methyl	97.3 % (109 of 112)	94.6 % (53 of 56)	100.0 % (56 of 56)

1. entity 1

GSDTQLFNRA VSMVEKNKDI RSLLQCDDGI TGKERLKAYG ELITNDKWTR NRPIVSTKKL DKEGRTHHYM RFHVESKKKI ALVHLEAKES KQNYQPDFIN MYVDVPGEKR YYLIK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

Release date

2019-06-12

Citation

Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study
Bala, S., Shinya, S., Srivastava, A., Ishikawa, M., Shimada, A., Kobayashi, N., Kojima, C., Tama, F., Miyashita, O., Kohda, D.
Biochim. Biophys. Acta. Gen. Subj. (2020), 1864, 129418-129418, PubMed 31449839 , DOI 10.1016/j.bbagen.2019.129418 , Abstract

Related entities 1. Mitochondrial import inner membrane translocase subunit TIM21, : 1 : 4 : 14 entities Detail

Interaction partners 1. Mitochondrial import inner membrane translocase subunit TIM21, : 16 interactors Detail

More details for 16 interactors identified by 6 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 3D HNCACB

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE III - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

7 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

8 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

9 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

10 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE III - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 6.5, Details 323 uM [U-13C; U-15N] Tim21, 20 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Tim21	[U-13C; U-15N]	protein	323 uM
2	TRIS	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	50 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr36264_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	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr36264_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1400		99.1 (chain: 1, length: 115)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 115, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 786
  - ¹³C chemical shifts: 494
  - ¹⁵N chemical shifts: 120
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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 Protein transport, membrane, mitochondria, translocation