BMRBj - BMREntryMaster

Found 1 Document (0.431 seconds)

BMRB: 34487

7A4L

NMR solution structure of the Iron-Sulfur protein PioC from Rhodopseudomonas palustris TIE-1

Authors

Cantini, F., Trindade, I.

Assembly

PioC

Entity

1. PioC, entity 1 (polymer), 54 monomers, 5872.568 Da Detail

VTKKASHKDA GYQESPNGAK RCGTCRQFRP PSSCITVESP ISENGWCRLY AGKA

2. PioC, entity SF4 (non-polymer), 351.640 Da

Total weight

6224.208 Da

Max. entity weight

5872.568 Da

Source organism

Rhodopseudomonas palustris TIE-1

Exptl. method

solution NMR

Refine. method

torsion angle dynamicsmolecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.2 %, Completeness (bb): 97.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.2 % (577 of 606)	93.1 % (296 of 318)	97.8 % (224 of 229)	96.6 % (57 of 59)
Backbone	97.8 % (309 of 316)	96.3 % (105 of 109)	98.7 % (155 of 157)	98.0 % (49 of 50)
Sidechain	92.9 % (315 of 339)	91.4 % (191 of 209)	95.9 % (116 of 121)	88.9 % (8 of 9)
Aromatic	100.0 % (42 of 42)	100.0 % (21 of 21)	100.0 % (20 of 20)	100.0 % (1 of 1)
Methyl	83.3 % (30 of 36)	77.8 % (14 of 18)	88.9 % (16 of 18)

1. entity 1

VTKKASHKDA GYQESPNGAK RCGTCRQFRP PSSCITVESP ISENGWCRLY AGKA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	PioC	natural abundance	500 (±0.2) uM
5	potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	300 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 150 uM [U-99% 15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	PioC	[U-99% 15N]	150 (±0.2) uM
8	potassium phosphate buffer	natural abundance	50 mM
9	NaCl	natural abundance	300 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6XYV, Strand ID: A Detail

Release date

2020-05-05

Citation

PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems
Trindade, I., Invernici, M., Cantini, F., Louro, R., Piccioli, M.
FEBS J. (2021), 288, 3010-3023, PubMed 33124176 , DOI 10.1111/febs.15615 , Abstract

Related entities 1. PioC, entity 1, : 1 : 2 : 4 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

2 3D HNCO

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

3 3D HNCA

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

4 3D CBCANH

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

5 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

6 3D HNCACO

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

7 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

8 3D HNHA

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

9 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

10 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	PioC	natural abundance	500 (±0.2) uM
5	potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	300 mM

11 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	PioC	natural abundance	500 (±0.2) uM
5	potassium phosphate buffer	natural abundance	50 mM
6	NaCl	natural abundance	300 mM

12 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

13 2D CON

Instrument

Bruker AVANCE - 700 MHz Console NEO

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

14 2D relaxation experiments

Instrument

Bruker AVANCE - 500 MHz Console NEO

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 150 uM [U-99% 15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	PioC	[U-99% 15N]	150 (±0.2) uM
8	potassium phosphate buffer	natural abundance	50 mM
9	NaCl	natural abundance	300 mM

15 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE - 950 MHz Console NEO

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 500 uM [U-13C; U-15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PioC	[U-13C; U-15N]	500 (±0.2) uM
2	potassium phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	300 mM

16 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.6, Details 150 uM [U-99% 15N] PioC, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	PioC	[U-99% 15N]	150 (±0.2) uM
8	potassium phosphate buffer	natural abundance	50 mM
9	NaCl	natural abundance	300 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34487_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: bmr34487_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	615		100.0 (chain: 1, length: 54)
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: 54, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 231
  - ¹H chemical shifts: 324
  - ¹⁵N chemical shifts: 60
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
12	TYR	CG	129.55
12	TYR	CZ	158.57
13	GLN	CD	181.47
16	PRO	N	130.36
17	ASN	CG	176.64
28	PHE	CG	138.69
31	PRO	N	128.95
40	PRO	N	136.15
46	TRP	CG	113.8
46	TRP	CE2	139.47

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	229	224	97.8
¹H chemical shifts	318	296	93.1
¹⁵N chemical shifts	59	57	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	108	108	100.0
¹H chemical shifts	109	105	96.3
¹⁵N chemical shifts	50	49	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	121	116	95.9
¹H chemical shifts	209	191	91.4
¹⁵N chemical shifts	9	8	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	18	16	88.9
¹H chemical shifts	18	14	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	20	20	100.0
¹H chemical shifts	21	21	100.0
¹⁵N chemical shifts	1	1	100.0

Keywords ELECTRON TRANSPORT, iron-sulphur protein, metallo proteins, paramagnetic NMR, paramagnetic protein, solution structure by NMR

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Found 1 Document (0.431 seconds)

BMRB: 34487

Sample #1

Sample #2

Sample #3

Related entities 1. PioC, entity 1, : 1 : 2 : 4 entities Detail

Experiments performed 16 experiments Detail

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Chemical shift validation 4 contents Detail