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Found 1 Document (0.479 seconds)

BMRB: 30370

6BI6

Solution NMR structure of uncharacterized protein YejG representing the first structure from PF13989

Authors

Mohanty, B., Finn, T.J., Macindoe, I., Zhong, J., Patrick, W.M., Mackay, J.P.

Assembly

Uncharacterized protein YejG

Entity

1. Uncharacterized protein YejG (polymer, Thiol state: all free), 115 monomers, 12548.07 Da Detail

GPTSLQLSIV HRLPQNYRWS AGFAGSKVEP IPQNGPCGDN SLVALKLLSP DGDNAWSVMY KLSQALSDIE VPCSVLECEG EPCLFVNRQD EFAATCRLKN FGVAIAEPFS NYNPF

Formula weight

12548.07 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 86.1 %, Completeness (bb): 92.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.1 % (1130 of 1313)	85.5 % (583 of 682)	85.9 % (439 of 511)	90.0 % (108 of 120)
Backbone	92.4 % (619 of 670)	91.7 % (209 of 228)	92.9 % (313 of 337)	92.4 % (97 of 105)
Sidechain	81.5 % (611 of 750)	82.4 % (374 of 454)	80.4 % (226 of 281)	73.3 % (11 of 15)
Aromatic	58.0 % (65 of 112)	75.0 % (42 of 56)	38.9 % (21 of 54)	100.0 % (2 of 2)
Methyl	89.0 % (105 of 118)	89.8 % (53 of 59)	88.1 % (52 of 59)

1. entity 1

GPTSLQLSIV HRLPQNYRWS AGFAGSKVEP IPQNGPCGDN SLVALKLLSP DGDNAWSVMY KLSQALSDIE VPCSVLECEG EPCLFVNRQD EFAATCRLKN FGVAIAEPFS NYNPF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 600 uM [U-13C,15N] YejG, 20 mM Bi-tris, 50 mM NaCl, 1 mM TCEP, 0.2 mM PMSF, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.71 ppm, Outliers: 2 Detail

Release date

2017-11-27

Citation

The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G
Mohanty, B., Hanson-Manful, P., Finn, T.J., Chambers, C.R., McKellar, J., Macindoe, I., Helder, S., Setiyaputra, S., Zhong, Y., Mackay, J.P., Patrick, W.M.
Proteins (2019), 87, 699-705, PubMed 30958578 , DOI 10.1002/prot.25687 , Abstract

Related entities 1. Uncharacterized protein YejG, : 2 : 1 entities Detail

Experiments performed 16 experiments Detail

1 2D [15N,1H]-HSQC

Instrument

Bruker Avance III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 600 uM [U-13C,15N] YejG, 20 mM Bi-tris, 50 mM NaCl, 1 mM TCEP, 0.2 mM PMSF, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

2 3D 15N-resolved [1H,1H]-NOESY

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

3 3D 13Cali-resolved [1H,1H]-NOESY

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

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

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

5 2D [13Cali,1H]-HSQC (multiplicity edited)

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

6 2D [13Caro,1H]-HSQC

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

7 2D 1H-1H NOESY

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

8 3D NUS HNCA

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

9 3D NUS HNCACB

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

10 3D NUS CBCA(CO)NH

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

11 3D NUS HN(CA)CO

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

12 3D NUS HNCO

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

13 3D NUS HBHA(CO)NH

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

14 3D NUS HNHA

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

15 3D NUS (H)CC(CO)NH

Instrument

Bruker Avance III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

16 15N{1H}-NOE

Instrument

Bruker Avance III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Bi-tris	natural abundance	20 mM
2	NaCl	natural abundance	50 mM
3	PMSF	natural abundance	0.2 mM
4	TCEP	natural abundance	1 mM
5	YejG	[U-13C; U-15N]	600 uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30370_6bi6.nef
Input source #2: Coordindates	6bi6.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

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
GPTSLQLSIVHRLPQNYRWSAGFAGSKVEPIPQNGPCGDNSLVALKLLSPDGDNAWSVMYKLSQALSDIEVPCSVLECEGEPCLFVNRQDEFAATCRLKN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPTSLQLSIVHRLPQNYRWSAGFAGSKVEPIPQNGPCGDNSLVALKLLSPDGDNAWSVMYKLSQALSDIEVPCSVLECEGEPCLFVNRQDEFAATCRLKN
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------110----
FGVAIAEPFSNYNPF
|||||||||||||||
FGVAIAEPFSNYNPF
-------110-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_30370_6bi6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1122		93.0 (chain: A, length: 115)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1505 (1)	noe	92.2 (chain: A, length: 115)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	56 (1)	hbond	31.3 (chain: A, length: 115)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	109 (109)	.	62.6 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 93.0%
- Total number of assignments
  - ¹H chemical shifts: 577
  - ¹³C chemical shifts: 439
  - ¹⁵N chemical shifts: 106
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	682	577	84.6
¹³C chemical shifts	511	439	85.9
¹⁵N chemical shifts	124	106	85.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	228	210	92.1
¹³C chemical shifts	230	213	92.6
¹⁵N chemical shifts	105	96	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	454	367	80.8
¹³C chemical shifts	281	226	80.4
¹⁵N chemical shifts	19	10	52.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	56	93.3
¹³C chemical shifts	60	55	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	42	75.0
¹³C chemical shifts	54	21	38.9
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 92.2%
- Total number of restraints: 1505
- Weight of restraints: 1.0 (1505)
- Potential type of restraints: upper-bound-parabolic (1505)
- 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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 31.3%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: upper-bound-parabolic (56)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 62.6%
- Total number of restraints: 109
- Total number of restraints per polymer type: 109
- Weight of restraints: 1.0 (109)
- Potential type of restraints: square-well-parabolic (109)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PF13989, UNKNOWN FUNCTION, YejG

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Found 1 Document (0.479 seconds)

BMRB: 30370

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Uncharacterized protein YejG, : 2 : 1 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 5 contents Detail