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BMRB: 16057

2KBZ

NMR structure of protein gp15 of bacteriophage SPP1

Authors

Gallopin, M., Gilquin, B., Zinn-Justin, S.

Assembly

gp15

Entity

1. gp15 (polymer, Thiol state: all free), 99 monomers, 11254.83 Da Detail

QRVKRLLSIT NDKHDEYLTE MVPLLVEFAK DECHNPFIDK DGNESIPSGV LIFVAKAAQF YMTNAGLTGR SMDTVSYNFA TEIPSTILKK LNPYRKMAR

Formula weight

11254.83 Da

Source organism

Bacillus phage SPP1

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 86.9 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.9 % (1023 of 1177)	88.6 % (543 of 613)	83.5 % (386 of 462)	92.2 % (94 of 102)
Backbone	93.8 % (548 of 584)	92.9 % (183 of 197)	94.9 % (278 of 293)	92.6 % (87 of 94)
Sidechain	82.6 % (568 of 688)	86.8 % (361 of 416)	75.8 % (200 of 264)	87.5 % (7 of 8)
Aromatic	34.4 % (31 of 90)	62.2 % (28 of 45)	6.7 % (3 of 45)
Methyl	99.1 % (111 of 112)	98.2 % (55 of 56)	100.0 % (56 of 56)

1. gp15

QRVKRLLSIT NDKHDEYLTE MVPLLVEFAK DECHNPFIDK DGNESIPSGV LIFVAKAAQF YMTNAGLTGR SMDTVSYNFA TEIPSTILKK LNPYRKMAR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

LACS Plot; CA

Referencing offset: 2.61 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 2.61 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 2.24 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-05-19

Citation

Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating
Lhuillier, S., Gallopin, M., Gilquin, B., Brasiles, S., Lancelot, N., Letellier, G., Gilles, M., Dethan, G., Orlova, E.V., Couprie, J., Tavares, P., Zinn-Justin, S.
Proc. Natl. Acad. Sci. U. S. A. (2009), 106, 8507-8512, PubMed 19433794 , DOI 10.1073/pnas.0812407106 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 16068 released on 2009-05-19
Title gp16

Related entities 1. gp15, : 1 : 5 : 2 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

2 2D H-D exchange

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

3 3D HNHA

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

5 2D 1H-15N nOe transfer

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

6 3D 1H-15N NOESY

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	gp15	[U-100% 15N]		0.5 mM

7 3D HNCO

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

8 3D HNCA

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

9 3D 1H-13C NOESY

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

10 3D HNCACO

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

11 3D HNCACB

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

12 3D CBCA(CO)NH

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

13 3D HBHA(CO)NH

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

14 3D HCCH COSY

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

15 3D HCCH TOCSY

Instrument

Bruker Avance 2 - 600 MHz With Cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
2	gp15	[U-100% 13C; U-100% 15N]		0.5 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16057_2kbz.nef
Input source #2: Coordindates	2kbz.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

-40-------50--------60--------70--------80--------90-------100-------110-------120-------130-------
QRVKRLLSITNDKHDEYLTEMVPLLVEFAKDECHNPFIDKDGNESIPSGVLIFVAKAAQFYMTNAGLTGRSMDTVSYNFATEIPSTILKKLNPYRKMAR
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QRVKRLLSITNDKHDEYLTEMVPLLVEFAKDECHNPFIDKDGNESIPSGVLIFVAKAAQFYMTNAGLTGRSMDTVSYNFATEIPSTILKKLNPYRKMAR
--------10--------20--------30--------40--------50--------60--------70--------80--------90---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_16057_2kbz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1021		97.0 (chain: A, length: 99)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3398 (1)	noe	97.0 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 97.0%
- Total number of assignments
  - ¹H chemical shifts: 546
  - ¹³C chemical shifts: 382
  - ¹⁵N chemical shifts: 93
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 97.0%
- Total number of restraints: 3348
- Weight of restraints: 1.0 (3348)
- Potential type of restraints: square-well-parabolic (3348)
- Range of distance target values: 1.9, 5.61 (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 three alpha-helix bundle