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BMRB: 18437

2LSM

Solution structure of gpFI C-terminal domain

Authors

Popovic, A., Wu, B., Edwards, A.M., Davidson, A.R., Maxwell, K.L.

Assembly

gpFI C-terminal domain

Entity

1. gpFI C-terminal domain (polymer, Thiol state: not present), 61 monomers, 6488.400 Da Detail

PDTVILDTSE LVTVVALVKL HTDALHATRD EPVAFVLPGT AFRVSAGVAA EMTERGLARM Q

Formula weight

6488.4 Da

Source organism

Escherichia virus Lambda

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.2 %, Completeness (bb): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.2 % (562 of 660)	94.6 % (314 of 332)	70.3 % (189 of 269)	100.0 % (59 of 59)
Backbone	83.1 % (299 of 360)	98.4 % (120 of 122)	67.2 % (121 of 180)	100.0 % (58 of 58)
Sidechain	89.1 % (319 of 358)	92.4 % (194 of 210)	84.4 % (124 of 147)	100.0 % (1 of 1)
Aromatic	32.1 % (9 of 28)	64.3 % (9 of 14)	0.0 % (0 of 14)
Methyl	91.0 % (91 of 100)	92.0 % (46 of 50)	90.0 % (45 of 50)

1. polypeptide

PDTVILDTSE LVTVVALVKL HTDALHATRD EPVAFVLPGT AFRVSAGVAA EMTERGLARM Q

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
6	gpFI	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	potassium chloride	natural abundance		250 mM
9	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-07-22

Citation

Structural and biochemical characterization of phage λ FI protein (gpFI) reveals a novel mechanism of DNA packaging chaperone activity
Popovic, A., Wu, B., Arrowsmith, C.H., Edwards, A.M., Davidson, A.R., Maxwell, K.L.
J. Biol. Chem. (2012), 287, 32085-32095, PubMed 22801427 , DOI 10.1074/jbc.M112.378349 , Abstract

Entries sharing articles Swiss-Prot: 2 entries Detail

  Swiss-Prot: P03709 released on 1986-07-21
    Title FI_LAMBD Entity DNA-packaging protein FI
  Swiss-Prot: P03713 released on 1986-07-21
    Title CAPSD_LAMBD Entity Major capsid protein

Related entities 1. gpFI C-terminal domain, : 1 : 1 : 10 entities Detail

Interaction partners 1. gpFI C-terminal domain, : 4 interactors Detail

More details for 4 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

2 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

3 3D HNCO

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

4 3D HNCACB

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

6 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

7 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
6	gpFI	[U-100% 13C; U-100% 15N]		1 mM
7	sodium phosphate	natural abundance		25 mM
8	potassium chloride	natural abundance		250 mM
9	D2O	natural abundance		100 %

8 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz Quebec/Eastern Canada High Field NMR Facility

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	gpFI	[U-99% 13C; U-99% 15N]		1 mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		250 mM
4	H2O	natural abundance		90 mM
5	D2O	natural abundance		10 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18437_2lsm.nef
Input source #2: Coordindates	2lsm.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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	61	0	0	100.0

Content subtype: combined_18437_2lsm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	566		100.0 (chain: A, length: 61)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2084 (1)	noe	98.4 (chain: A, length: 61)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	74 (74)	.	80.3 (chain: A, length: 61)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 319
  - ¹³C chemical shifts: 187
  - ¹⁵N chemical shifts: 60
- 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: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 98.4%
- Total number of restraints: 2084
- Weight of restraints: 1.0 (2084)
- Potential type of restraints: upper-bound-parabolic (2084)
- Range of distance target values: 2.28, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 61, Sequence coverage: 80.3%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA packaging, gene product FI, phage lambda, Protein