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BMRB: 26844

6MPO

NMR assignments for the insertion domain of bacteriophage Sf6 coat protein

Authors

Tripler, T.N., Teschke, C.M., Alexandrescu, A.T.

Assembly

procapsid

Entity

1. procapsid (polymer, Thiol state: not present), 124 monomers, 12885.98 Da Detail

GAFGGTLTVK TQPTVTYNAV KDSYQFTVTL TGATASVTGF LKAGDQVKFT NTYWLQQQTK QALYNGATPI SFTATVTADA NSDSGGDVTV TLSGVPIYDT TNPQYNSVSR QVEAGDAVSV VGTA

Formula weight

12885.98 Da

Source organism

Bacteriophage sp.

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 89.1 %, Completeness (bb): 96.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.1 % (1179 of 1323)	90.5 % (599 of 662)	85.3 % (448 of 525)	97.1 % (132 of 136)
Backbone	96.1 % (707 of 736)	94.5 % (242 of 256)	96.4 % (347 of 360)	98.3 % (118 of 120)
Sidechain	83.3 % (582 of 699)	87.9 % (357 of 406)	76.2 % (211 of 277)	87.5 % (14 of 16)
Aromatic	43.6 % (48 of 110)	80.0 % (44 of 55)	7.4 % (4 of 54)	0.0 % (0 of 1)
Methyl	93.2 % (151 of 162)	92.6 % (75 of 81)	93.8 % (76 of 81)

1. Sf6id

GAFGGTLTVK TQPTVTYNAV KDSYQFTVTL TGATASVTGF LKAGDQVKFT NTYWLQQQTK QALYNGATPI SFTATVTADA NSDSGGDVTV TLSGVPIYDT TNPQYNSVSR QVEAGDAVSV VGTA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
6	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: 0.43 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 0.43 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.22 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 6MPO, Strand ID: A Detail

Release date

2016-07-04

Citation

NMR assignments for the insertion domain of bacteriophage Sf6 coat protein
Tripler, T.N., Teschke, C.M., Alexandresu, A.T.
Biomol. NMR Assign. (2017), 11, 35-38, PubMed 27798771 , DOI 10.1007/s12104-016-9716-5 , Abstract

Related entities 1. procapsid, : 1 : 1 : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC NH2 only

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 HNCACO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	insertion domain	[U-100% 15N]		1.5 mM
2	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
6	D2O	natural abundance		100 %

8 3D CCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
6	D2O	natural abundance		100 %

9 2D DQF-COSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
6	D2O	natural abundance		100 %

10 2D 1H-1H TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
6	D2O	natural abundance		100 %

11 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	insertion domain	[U-100% 13C; U-100% 15N]		2.1 mM
6	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_26844_6mpo.nef
Input source #2: Coordindates	6mpo.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

------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-
GAFGGTLTVKTQPTVTYNAVKDSYQFTVTLTGATASVTGFLKAGDQVKFTNTYWLQQQTKQALYNGATPISFTATVTADANSDSGGDVTVTLSGVPIYDT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAFGGTLTVKTQPTVTYNAVKDSYQFTVTLTGATASVTGFLKAGDQVKFTNTYWLQQQTKQALYNGATPISFTATVTADANSDSGGDVTVTLSGVPIYDT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------330-------340-------350---
TNPQYNSVSRQVEAGDAVSVVGTALEHHHHHH
||||||||||||||||||||||||||||||||
TNPQYNSVSRQVEAGDAVSVVGTALEHHHHHH
-------110-------120-------130--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	132	0	0	100.0

Content subtype: combined_26844_6mpo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1187		92.4 (chain: A, length: 132)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	778 (1)	noe	89.4 (chain: A, length: 132)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	707 (1)	noe	87.9 (chain: A, length: 132)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 92.4%
- Total number of assignments
  - ¹H chemical shifts: 607
  - ¹³C chemical shifts: 448
  - ¹⁵N chemical shifts: 132
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 89.4%
- Total number of restraints: 778
- Weight of restraints: 1.0 (778)
- Potential type of restraints: square-well-parabolic (778)
- Range of distance target values: 2.26, 5.46 (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: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 132, Sequence coverage: 87.9%
  - Total number of restraints: 707
  - Weight of restraints: 1.0 (707)
  - Potential type of restraints: square-well-parabolic (707)
  - Range of distance target values: 2.49, 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