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BMRB: 15252

2JPN

Solution Structure of T4 Bacteriophage Helicase Uvsw.1

Authors

Sivakolundu, S.G., Lee, T., White, S.W., Kriwacki, R.W.

Assembly

UvsW.1

Entity

1. UvsW.1 (polymer, Thiol state: all free), 79 monomers, 9084.951 Da Detail

GSHMLLEFKQ FLYEASIDEF MGKIASCQTL EGLEELEAYY KKRVKETELK DTDDISVRDA LAGKRAELED SDDEVEESF

Formula weight

9084.951 Da

Source organism

Escherichia virus T4

Exptl. method

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts, heteronucl_NOEs

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 76.3 %, Completeness (bb): 80.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.3 % (700 of 918)	78.7 % (376 of 478)	68.2 % (245 of 359)	97.5 % (79 of 81)
Backbone	80.8 % (383 of 474)	91.4 % (148 of 162)	67.8 % (158 of 233)	97.5 % (77 of 79)
Sidechain	75.1 % (390 of 519)	72.2 % (228 of 316)	79.6 % (160 of 201)	100.0 % (2 of 2)
Aromatic	29.4 % (20 of 68)	44.1 % (15 of 34)	14.7 % (5 of 34)
Methyl	85.9 % (67 of 78)	82.1 % (32 of 39)	89.7 % (35 of 39)

1. UvsW.1

GSHMLLEFKQ FLYEASIDEF MGKIASCQTL EGLEELEAYY KKRVKETELK DTDDISVRDA LAGKRAELED SDDEVEESF

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

LACS Plot; CA

Referencing offset: -0.35 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.35 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Heteronucl. NOE

72 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 Detail

Release date

2007-10-28

Citation

Crystallographic and NMR analyses of UvsW and UvsW.1 from bacteriophage T4
Kerr, I.D., Sivakolundu, S., Li, Z., Buchsbaum, J.C., Knox, L.A., Kriwacki, R., White, S.W.
J. Biol. Chem. (2007), 282, 34392-34400, PubMed 17878153 , DOI 10.1074/jbc.M705900200 , Abstract

Related entities 1. UvsW.1, : 1 : 1 : 6 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

3 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

4 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

8 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

9 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

12 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

13 2D 1H-15N HSQC, Steady state {1H}-15N NOE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	UvsW.1	[U-99% 13C; U-99% 15N]		1.66 (±0.1) mM
2	sodium phosphate			10 mM
3	NaCl			10 mM
4	DTT			1 mM
5	sodium azide			0.02 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15252_2jpn.nef
Input source #2: Coordindates	2jpn.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---------
GSHMLLEFKQFLYEASIDEFMGKIASCQTLEGLEELEAYYKKRVKETELKDTDDISVRDALAGKRAELEDSDDEVEESF
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMLLEFKQFLYEASIDEFMGKIASCQTLEGLEELEAYYKKRVKETELKDTDDISVRDALAGKRAELEDSDDEVEESF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0

Content subtype: combined_15252_2jpn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	685		96.2 (chain: A, length: 79)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2734 (1)	noe	93.7 (chain: A, length: 79)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	98 (98)	.	79.7 (chain: A, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 96.2%
- Total number of assignments
  - ¹H chemical shifts: 376
  - ¹³C chemical shifts: 231
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 93.7%
- Total number of restraints: 2734
- Weight of restraints: 1.0 (2734)
- Potential type of restraints: upper-bound-parabolic (2734)
- Range of distance target values: 2.2, 7.1 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 79.7%
- Total number of restraints: 98
- Total number of restraints per polymer type: 98
- Weight of restraints: 1.0 (98)
- Potential type of restraints: square-well-parabolic (98)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords bacteriophage helicase, uvsw