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BMRB: 25975

2NBG

Structure and Dynamics of the Geobacillus stearothermophilus IF2 G3-subdomain

Authors

Dongre, R., Folkers, G.E., Gualerzi, C.O., Boelens, R., Wienk, H.

Assembly

Geobacillus stearothermophilus IF2 G3-subdomain

Entity

1. Geobacillus stearothermophilus IF2 G3-subdomain (polymer, Thiol state: not present), 125 monomers, 13628.58 Da Detail

GSHMLDHLLE MILLVSEMEE LKANPNRRAV GTVIEAKLDK GRGPVATLLV QAGTLKVGDP IVVGTTYGRV RAMVNDSGRR VKEAGPSMPV EITGLHDVPQ AGDRFMVFED EKKARQIGEA RAQRQ

Formula weight

13628.58 Da

Source organism

Geobacillus stearothermophilus

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.6 %, Completeness: 76.8 %, Completeness (bb): 90.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.8 % (1083 of 1410)	74.5 % (549 of 737)	77.3 % (422 of 546)	88.2 % (112 of 127)
Backbone	90.2 % (666 of 738)	89.5 % (230 of 257)	90.6 % (328 of 362)	90.8 % (108 of 119)
Sidechain	66.2 % (519 of 784)	66.5 % (319 of 480)	66.2 % (196 of 296)	50.0 % (4 of 8)
Aromatic	10.0 % (4 of 40)	20.0 % (4 of 20)	0.0 % (0 of 20)
Methyl	84.4 % (130 of 154)	85.7 % (66 of 77)	83.1 % (64 of 77)

1. entity

GSHMLDHLLE MILLVSEMEE LKANPNRRAV GTVIEAKLDK GRGPVATLLV QAGTLKVGDP IVVGTTYGRV RAMVNDSGRR VKEAGPSMPV EITGLHDVPQ AGDRFMVFED EKKARQIGEA RAQRQ

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.22 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.22 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 5 Detail

LACS Plot; CO

Referencing offset: 0.42 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2016-07-17

Citation

A model for the interaction of the G3-subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit
Dongre, R., Folkers, G.E., Gualerzi, C.O., Boelens, R., Wienk, H.
Protein Sci. (2016), 25, 1722-1733, PubMed 27364543 , DOI 10.1002/pro.2977 , Abstract

Related entities 1. Geobacillus stearothermophilus IF2 G3-subdomain, : 1 : 1 : 138 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 3D HNCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

9 3D HBHACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	IF2-G3	[U-100% 13C; U-100% 15N]		0.15 mM
2	sodium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	glycerol	natural abundance		2 %
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25975_2nbg.nef
Input source #2: Coordindates	2nbg.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

390-----400-------410-------420-------430-------440-------450-------460-------470-------480-------49
GSHMLDHLLEMILLVSEMEELKANPNRRAVGTVIEAKLDKGRGPVATLLVQAGTLKVGDPIVVGTTYGRVRAMVNDSGRRVKEAGPSMPVEITGLHDVPQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMLDHLLEMILLVSEMEELKANPNRRAVGTVIEAKLDKGRGPVATLLVQAGTLKVGDPIVVGTTYGRVRAMVNDSGRRVKEAGPSMPVEITGLHDVPQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------500-------510----
AGDRFMVFEDEKKARQIGEARAQRQ
|||||||||||||||||||||||||
AGDRFMVFEDEKKARQIGEARAQRQ
-------110-------120-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_25975_2nbg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1049		91.2 (chain: A, length: 125)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2080 (1)	noe	90.4 (chain: A, length: 125)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	149 (149)	.	73.6 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 91.2%
- Total number of assignments
  - ¹H chemical shifts: 537
  - ¹³C chemical shifts: 402
  - ¹⁵N chemical shifts: 110
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 90.4%
- Total number of restraints: 2080
- Weight of restraints: 1.0 (2080)
- Potential type of restraints: square-well-parabolic (2080)
- Range of distance target values: 1.28, 2.75 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 73.6%
- Total number of restraints: 149
- Total number of restraints per polymer type: 149
- Weight of restraints: 1.0 (149)
- Potential type of restraints: square-well-parabolic (149)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords IF2, ribosome, translation initiation