BMRBj - BMREntryMaster

Found 1 Document (0.75 seconds)

BMRB: 34385

7AFQ

Solution Structure of ribosome-binding factor A (RbfA) under physiological conditions

Authors

Schedlbauer, A., Ochoa Lizarralde, B., Capuni, R., Iturrioz, I., Fucini, P., Connell, S.

Assembly

Ribosome-binding factor A

Entity

1. Ribosome-binding factor A (polymer, Thiol state: not present), 140 monomers, 15911.14 Da Detail

SAKEFGRPQR VAQEMQKEIA LILQREIKDP RLGMMTTVSG VEMSRDLAYA KVYVTFLNDK DEDAVKAGIK ALQEASGFIR SLLGKAMRLR IVPELTFFYD NSLVEGMRMS NLVTSVVKHD EERRVNPDDS KEDALEVLFQ

Formula weight

15911.14 Da

Source organism

Enterobacter sp. EC-NT1

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 84.7 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.7 % (1399 of 1652)	83.5 % (722 of 865)	86.3 % (553 of 641)	84.9 % (124 of 146)
Backbone	90.5 % (753 of 832)	90.1 % (255 of 283)	91.8 % (379 of 413)	87.5 % (119 of 136)
Sidechain	81.0 % (772 of 953)	80.2 % (467 of 582)	83.1 % (300 of 361)	50.0 % (5 of 10)
Aromatic	15.9 % (14 of 88)	22.7 % (10 of 44)	9.1 % (4 of 44)
Methyl	97.0 % (159 of 164)	93.9 % (77 of 82)	100.0 % (82 of 82)

1. entity 1

SAKEFGRPQR VAQEMQKEIA LILQREIKDP RLGMMTTVSG VEMSRDLAYA KVYVTFLNDK DEDAVKAGIK ALQEASGFIR SLLGKAMRLR IVPELTFFYD NSLVEGMRMS NLVTSVVKHD EERRVNPDDS KEDALEVLFQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.6, Details 400 uM [U-98% 13C; U-98% 15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

Protein Blocks Logo

Calculated from 20 models in PDB: 6R8D, Strand ID: A Detail

Release date

2020-05-25

Citation

A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit
Schedlbauer, A., Iturrioz, I., Ochoa-Lizarralde, B., Diercks, T., Lopez-Alonso, J.P., Lavin, J.L., Kaminishi, T., Capuni, R., Dhimole, N., de Astigarraga, E., Gil-Carton, D., Fucini, P., Connell, S.R.
Sci. Adv. (2021), 7, eabf7547-eabf7547, PubMed 34088665 , DOI 10.1126/sciadv.abf7547 , Abstract

Related entities 1. Ribosome-binding factor A, : 1 : 9 : 103 entities Detail

Interaction partners 1. Ribosome-binding factor A, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.6, Details 400 uM [U-98% 13C; U-98% 15N] RbfA, 10 mM HEPES, 6 mM MgCl2, 30 mM NH4Cl, 75 uM TCEP, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

2 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

3 3D HNCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

4 3D HNCACB

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

5 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

6 3D HN(CO)CA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

7 3D HNCAHA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

8 3D HCCH-TOCSY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

9 3D HN(CA)CO

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

10 3D HNH NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

11 3D CNH NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

12 3D HN(CO)CAHA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

13 3D HCH NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	RbfA	[U-98% 13C; U-98% 15N]	400 uM
2	HEPES	natural abundance	10 mM
3	MgCl2	natural abundance	6 mM
4	NH4Cl	natural abundance	30 mM
5	TCEP	natural abundance	75 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34385_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	OK

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr34385_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	1472		90.7 (chain: 1, length: 140)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 140, Sequence coverage: 90.7%
- Total number of assignments
  - ¹H chemical shifts: 836
  - ¹³C chemical shifts: 522
  - ¹⁵N chemical shifts: 114
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	865	684	79.1
¹³C chemical shifts	641	522	81.4
¹⁵N chemical shifts	157	114	72.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	283	242	85.5
¹³C chemical shifts	280	237	84.6
¹⁵N chemical shifts	136	109	80.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	582	442	75.9
¹³C chemical shifts	361	285	78.9
¹⁵N chemical shifts	21	5	23.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	76	85.4
¹³C chemical shifts	89	84	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	7	15.9
¹³C chemical shifts	44	0	0.0

Keywords RIBOSOMAL PROTEIN, Ribosome Assembly Factor

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Found 1 Document (0.75 seconds)

BMRB: 34385

Sample

Related entities 1. Ribosome-binding factor A, : 1 : 9 : 103 entities Detail

Interaction partners 1. Ribosome-binding factor A, : 2 interactors Detail

Experiments performed 13 experiments Detail

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Chemical shift validation 3 contents Detail