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BMRB: 15807

2K4Q

The Solution Structure of gpV, the Major Tail Protein from Bacteriophage Lambda

Authors

Pell, L.G., Kanelis, V., Howell, P., Davidson, A.R.

Assembly

gpV

Entity

1. gpV (polymer, Thiol state: not present), 156 monomers, 16881.64 Da Detail

GAMMPVPNPT MPVKGAGTTL WVYKGSGDPY ANPLSDVDWS RLAKVKDLTP GELTAESYDD SYLDDEDADW TATGQGQKSA GDTSFTLAWM PGEQGQQALL AWFNEGDTRA YKIRFPNGTV DVFRGWVSSI GKAVTAKEVI TRTVKVTNVG RPSMAE

Formula weight

16881.64 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 84.0 %, Completeness (bb): 90.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.0 % (1455 of 1733)	85.5 % (762 of 891)	80.3 % (546 of 680)	90.7 % (147 of 162)
Backbone	90.7 % (831 of 916)	92.1 % (293 of 318)	88.9 % (402 of 452)	93.2 % (136 of 146)
Sidechain	78.7 % (753 of 957)	81.8 % (469 of 573)	74.2 % (273 of 368)	68.8 % (11 of 16)
Aromatic	42.8 % (65 of 152)	60.5 % (46 of 76)	18.6 % (13 of 70)	100.0 % (6 of 6)
Methyl	88.7 % (142 of 160)	90.0 % (72 of 80)	87.5 % (70 of 80)

1. gpV protein

GAMMPVPNPT MPVKGAGTTL WVYKGSGDPY ANPLSDVDWS RLAKVKDLTP GELTAESYDD SYLDDEDADW TATGQGQKSA GDTSFTLAWM PGEQGQQALL AWFNEGDTRA YKIRFPNGTV DVFRGWVSSI GKAVTAKEVI TRTVKVTNVG RPSMAE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

Sample #2

Solvent system 90% D2O, 10% H2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
7	gpV protein	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	90-99 %
9	DSS	natural abundance	0.6 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	200 mM
12	sodium azide	natural abundance	0.1 %

LACS Plot; CA

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

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.36 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4Q, Strand ID: A Detail

Release date

2008-11-13

Citation

The phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system
Pell, L.G., Kanelis, V., Donaldson, L.W., Howell, L., Davidson, A.R.
Proc. Natl. Acad. Sci. U. S. A. (2009), 106, 4160-4165, PubMed 19251647 , DOI 10.1073/pnas.0900044106 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P03733 released on 1986-07-21
Title TUBE_LAMBD Entity Tail tube protein

Related entities 1. gpV, : 1 : 3 entities Detail

Interaction partners 1. gpV, : 6 interactors Detail

More details for 6 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

2 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

3 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

7 3D HCCH-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% D2O, 10% H2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
7	gpV protein	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	90-99 %
9	DSS	natural abundance	0.6 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	200 mM
12	sodium azide	natural abundance	0.1 %

9 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

10 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	DSS	natural abundance	0.6 mM
3	sodium chloride	natural abundance	200 mM
4	D2O	natural abundance	8-10 %
5	sodium azide	natural abundance	0.1 %
6	gpV protein	[U-100% 13C; U-100% 15N]	1 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15807_2k4q.nef
Input source #2: Coordindates	2k4q.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

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

-------110-------120-------130-------140-------150------
AWFNEGDTRAYKIRFPNGTVDVFRGWVSSIGKAVTAKEVITRTVKVTNVGRPSMAE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AWFNEGDTRAYKIRFPNGTVDVFRGWVSSIGKAVTAKEVITRTVKVTNVGRPSMAE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	156	0	0	100.0

Content subtype: combined_15807_2k4q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1468		97.4 (chain: A, length: 156)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2276 (1)	noe	95.5 (chain: A, length: 156)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 779
  - ¹³C chemical shifts: 540
  - ¹⁵N chemical shifts: 149
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	PRO	N	141.218
9	PRO	N	138.875
12	PRO	N	139.222

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	891	764	85.7
¹³C chemical shifts	680	539	79.3
¹⁵N chemical shifts	168	146	86.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	318	295	92.8
¹³C chemical shifts	312	265	84.9
¹⁵N chemical shifts	146	136	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	573	469	81.8
¹³C chemical shifts	368	274	74.5
¹⁵N chemical shifts	22	10	45.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	75	88.2
¹³C chemical shifts	85	71	83.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	46	60.5
¹³C chemical shifts	70	13	18.6
¹⁵N chemical shifts	6	6	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: 156, Sequence coverage: 95.5%
- Total number of restraints: 2274
- Weight of restraints: 1.0 (2274)
- Potential type of restraints: upper-bound-parabolic (2274)
- Range of distance target values: 2.21, 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

Keywords Bacteriophage Lambda, gpV, Major tail protein, NMR

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Found 1 Document (0.956 seconds)

BMRB: 15807

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. gpV, : 1 : 3 entities Detail

Interaction partners 1. gpV, : 6 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail