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Found 1 Document (0.842 seconds)

BMRB: 17689

2LE2

Novel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition

Authors

Asensio, J., Perez-Lago, L., M. Lazaro, J., Gonzalez, C., Serrano-Heras, G., Salas, M.

Assembly

Uracil-DNA glycosylase inhibitor p56

Entity

1. Uracil-DNA glycosylase inhibitor p56 (polymer, Thiol state: not present), 56 monomers, 6565.261 × 2 Da Detail

MVQNDFVDSY DVTMLLQDDD GKQYYEYHKG LSLSDFEVLY GNTADEIIKL RLDKVL

Total weight

13130.522 Da

Max. entity weight

6565.261 Da

Source organism

Bacillus virus phi29

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.6 %, Completeness (bb): 96.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	92.6 % (375 of 405)	92.2 % (317 of 344)	95.1 % (58 of 61)
Backbone	96.5 % (165 of 171)	97.4 % (112 of 115)	94.6 % (53 of 56)
Sidechain	89.7 % (210 of 234)	89.5 % (205 of 229)	100.0 % (5 of 5)
Aromatic	56.3 % (18 of 32)	56.3 % (18 of 32)
Methyl	100.0 % (33 of 33)	100.0 % (33 of 33)

1. p56

MVQNDFVDSY DVTMLLQDDD GKQYYEYHKG LSLSDFEVLY GNTADEIIKL RLDKVL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
1	p56	natural abundance	0.5 mM
2	sodium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	10 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
6	p56	[U-98% 13C; U-98% 15N]	0.5 mM
7	sodium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	10 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	90 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
11	p56	natural abundance	0.5 mM
12	sodium chloride	natural abundance	100 mM
13	potassium phosphate	natural abundance	10 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	90 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LE2, Strand ID: A, B Detail

Release date

2012-02-21

Citation

Novel dimeric structure of phage φ29-encoded protein p56: insights into uracil-DNA glycosylase inhibition
Asensio, J., Perez-Lago, L., Lazaro, J.M., Gonzalez, C., Serrano-Heras, G., Salas, M.
Nucleic Acids Res. (2011), 39, 9779-9788, PubMed 21890898 , DOI 10.1093/nar/gkr667 , Abstract

Related entities 1. Uracil-DNA glycosylase inhibitor p56, : 1 : 1 : 8 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
1	p56	natural abundance	0.5 mM
2	sodium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	10 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	90 %

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
1	p56	natural abundance	0.5 mM
2	sodium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	10 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	90 %

3 2D 1H-1H COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
1	p56	natural abundance	0.5 mM
2	sodium chloride	natural abundance	100 mM
3	potassium phosphate	natural abundance	10 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	90 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
11	p56	natural abundance	0.5 mM
12	sodium chloride	natural abundance	100 mM
13	potassium phosphate	natural abundance	10 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	90 %

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
6	p56	[U-98% 13C; U-98% 15N]	0.5 mM
7	sodium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	10 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	90 %

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
6	p56	[U-98% 13C; U-98% 15N]	0.5 mM
7	sodium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	10 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	90 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5

#	Name	Isotope labeling	Concentration
6	p56	[U-98% 13C; U-98% 15N]	0.5 mM
7	sodium chloride	natural abundance	100 mM
8	potassium phosphate	natural abundance	10 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	90 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17689_2le2.nef
Input source #2: Coordindates	2le2.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------
MVQNDFVDSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKVL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVQNDFVDSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKVL

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50------
MVQNDFVDSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKVL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVQNDFVDSYDVTMLLQDDDGKQYYEYHKGLSLSDFEVLYGNTADEIIKLRLDKVL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0
B	B	56	0	0	100.0

Content subtype: combined_17689_2le2.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	381		100.0 (chain: A, length: 56)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1380 (1)	noe	98.2 (chain: A, length: 56), 98.2 (chain: B, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 323
  - ¹⁵N chemical shifts: 58
- Completeness of assignments
  - Entity_assemble_ID: A
- 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	344	323	93.9
¹⁵N chemical shifts	62	58	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	115	114	99.1
¹⁵N chemical shifts	56	53	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	229	209	91.3
¹⁵N chemical shifts	6	5	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	18	56.2

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 98.2%
  - Entity_assembly_ID: B, Chain length: 56, Sequence coverage: 98.2%
- Total number of restraints: 1380
- Weight of restraints: 1.0 (1380)
- Potential type of restraints: upper-bound-parabolic (1380)
- Range of distance target values: 2.6, 9.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords Bacillus subtilis, DNA mimicry, p56 solution structure, phage phi29, UDG inhibition

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Found 1 Document (0.842 seconds)

BMRB: 17689

Sample #1

Sample #2

Sample #3

Related entities 1. Uracil-DNA glycosylase inhibitor p56, : 1 : 1 : 8 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 3 contents Detail