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BMRB: 51391

8ACZ

NMR Evidence for the Conformational Change of Phage Protein gVp Upon Binding to ssDNA

Authors

Kedem, S., Hassid, R., Shamir, Y., Goldbourt, A.

Assembly

gVp

Entity

1. gVp (polymer, Thiol state: all free), 87 monomers, 9688.122 Da Detail

MIKVEIKPSQ AQFTTRSGVS RQGKPYSLNE QLCYVDLGNE YPVLVKITLD EGQPAYAPGL YTVHLSSFKV GQFGSLMIDR LRLVPAK

Formula weight

9688.122 Da

Source organism

Escherichia coli

Exptl. method

solid-state NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 92.6 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	92.6 % (461 of 498)	92.6 % (375 of 405)	92.5 % (86 of 93)
Backbone	96.4 % (323 of 335)	96.1 % (244 of 254)	97.5 % (79 of 81)
Sidechain	88.5 % (215 of 243)	90.0 % (208 of 231)	58.3 % (7 of 12)
Aromatic	81.1 % (30 of 37)	81.1 % (30 of 37)
Methyl	100.0 % (52 of 52)	100.0 % (52 of 52)

1. entity 1

MIKVEIKPSQ AQFTTRSGVS RQGKPYSLNE QLCYVDLGNE YPVLVKITLD EGQPAYAPGL YTVHLSSFKV GQFGSLMIDR LRLVPAK

Show sample condition

Sample #1

Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

Sample #2

Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

Release date

2022-04-06

Citation

Conformational Changes in Ff Phage Protein gVp upon Complexation with Its Viral Single-Stranded DNA Revealed Using Magic-Angle Spinning Solid-State NMR
Kedem, S., Hassid, R., Shamir, Y., Goldbourt, A.
Viruses (2022), 14, 1264-1264, PubMed 35746735 , DOI 10.3390/v14061264 , Abstract

Related entities 1. gVp, : 1 : 4 : 11 : 3 : 6 entities Detail

Experiments performed 18 experiments Detail

1 2D DARR5

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

2 2D DARR15

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

3 2D DARR100

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

4 2D DARR250

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

5 2D RFDR6

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

6 2D INADEQUATE

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

7 3D NCOCX25

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

8 3D NCACX25

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	gVp from fd bacteriophage	[U-100% 13C; U-100% 15N]		200 (±50.0) g/L
2	NaCl	natural abundance		200 mM
3	EDTA	natural abundance		1 mM
4	Tris-HCl	natural abundance		10 mM

9 2D DARR5

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

10 2D DARR15

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

11 2D DARR100

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

12 2D DARR300

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

13 2D NCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

14 2D NCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

15 3D NCOCX100

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

16 3D NCACX100

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

17 2D CORD150

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

18 2D CORD300

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 200mM NaCl, 1mM EDTA and 10mM Tris-HCl (pH 7.4), Temperature 263 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
5	gVp from fd bacteriophage	[1,3-13C]-glycerol		200 (±50.0) g/L
6	NaCl	natural abundance		200 mM
7	EDTA	natural abundance		1 mM
8	Tris-HCl	natural abundance		10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr51391_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: bmr51391_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	497		98.9 (chain: 1, length: 87)
1	Chemical shift references	chem_shift_reference_1	Warning	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 87, Sequence coverage: 98.9%

--------10--------20--------30--------40--------50--------60--------70--------80-------
MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPAK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
MIKVEIKPSQAQFTTRSGVSRQGKPYSLNEQLCYVDLGNEYPVLVKITLDEGQPAYAPGLYTVHLSSFKVGQFGSLMIDRLRLVPA 
--------10--------20--------30--------40--------50--------60--------70--------80------

Total number of assignments
- ¹³C chemical shifts: 405
- ¹⁵N chemical shifts: 92

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	GLU	CD	182.8
8	PRO	N	135.0
12	GLN	CD	180.2
13	PHE	CG	136.6
16	ARG	CZ	157.1
21	ARG	CZ	159.2
22	GLN	CD	172.7
25	PRO	N	137.6
29	ASN	CG	176.6
30	GLU	CD	183.7
31	GLN	CD	180.2
34	TYR	CZ	157.6
36	ASP	CG	180.5
40	GLU	CD	183.4
41	TYR	CZ	157.6
42	PRO	N	135.6
51	GLU	CD	182.8
53	GLN	CD	179.7
54	PRO	N	136.3
56	TYR	CG	130.6
56	TYR	CZ	156.4
58	PRO	N	132.6
61	TYR	CZ	157.6
64	HIS	CG	136.6
68	PHE	CG	139.7
72	GLN	CD	179.6
79	ASP	CG	178.2
82	ARG	CZ	166.6
85	PRO	N	137.2

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	405	382	94.3
¹⁵N chemical shifts	93	86	92.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	174	172	98.9
¹⁵N chemical shifts	81	79	97.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	231	210	90.9
¹⁵N chemical shifts	12	7	58.3

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	54	53	98.1

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	37	30	81.1

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