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BMRB: 15547

2JX5

Solution structure of ubiquitin domain N-terminal to S27a ribosome subunit from Giardia lamblia

Authors

Catic, A., Sun, Z.J., Ratner, D.M., Misaghi, S., Spooner, E., Samuelson, J., Wagner, G., Ploegh, H.L.

Assembly

GlUb(S27a)

Entity

1. GlUb(S27a) (polymer, Thiol state: not present), 69 monomers, 7299.275 Da Detail

MLVIVRLQDQ TLPFELPAGA RASQLSNLLS SSGMAFSLHT QGRVLSEAAE LNDKMVIDAF VPADGAGLE

Formula weight

7299.275 Da

Source organism

Giardia intestinalis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.0 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.0 % (685 of 761)	91.0 % (355 of 390)	88.6 % (265 of 299)	90.3 % (65 of 72)
Backbone	96.3 % (393 of 408)	97.1 % (136 of 140)	95.5 % (193 of 202)	97.0 % (64 of 66)
Sidechain	85.1 % (355 of 417)	87.6 % (219 of 250)	83.9 % (135 of 161)	16.7 % (1 of 6)
Aromatic	38.2 % (13 of 34)	76.5 % (13 of 17)	0.0 % (0 of 17)
Methyl	98.9 % (93 of 94)	97.9 % (46 of 47)	100.0 % (47 of 47)

1. GlUb(S27a)

MLVIVRLQDQ TLPFELPAGA RASQLSNLLS SSGMAFSLHT QGRVLSEAAE LNDKMVIDAF VPADGAGLE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details unlabeled

#	Name	Isotope labeling	Type	Concentration
6	GlUb(S27a)	natural abundance		1 mM
7	potassium phosphate	natural abundance		10 mM
8	sodium chloride	natural abundance		100 mM
9	D2O	natural abundance		100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 10% C13-labeled

#	Name	Isotope labeling	Type	Concentration
10	GlUb(S27a)	[U-10% 13C]		1 mM
11	potassium phosphate	natural abundance		10 mM
12	sodium chloride	natural abundance		100 mM
13	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 4 Detail

LACS Plot; CO

Referencing offset: 0.39 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2JX5, Strand ID: A Detail

Release date

2008-11-02

Citation

Sequence and structure evolved separately in a ribosomal ubiquitin variant
Catic, A., Sun, Z.J., Ratner, D.M., Misaghi, S., Spooner, E., Samuelson, J., Wagner, G., Ploegh, H.L.
EMBO J. (2007), 26, 3474-3483, PubMed 17599068 , DOI 10.1038/sj.emboj.7601772 , Abstract

Related entities 1. GlUb(S27a), : 1 : 4 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

2 3D HNCA

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

4 3D HNCO

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

5 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 750 MHz cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 15N/13C labeled

#	Name	Isotope labeling	Type	Concentration
1	GlUb(S27a)	[U-99% 13C; U-99% 15N]		1 mM
2	potassium phosphate	natural abundance		10 mM
3	sodium chloride	natural abundance		100 mM
4	D2O	natural abundance		10 %
5	H20	natural abundance		90 %

10 2D 1H-1H NOESY

Instrument

Bruker Avance - 750 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details unlabeled

#	Name	Isotope labeling	Type	Concentration
6	GlUb(S27a)	natural abundance		1 mM
7	potassium phosphate	natural abundance		10 mM
8	sodium chloride	natural abundance		100 mM
9	D2O	natural abundance		100 %

11 2D 1H-1H TOCSY

Instrument

Bruker Avance - 750 MHz cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details unlabeled

#	Name	Isotope labeling	Type	Concentration
6	GlUb(S27a)	natural abundance		1 mM
7	potassium phosphate	natural abundance		10 mM
8	sodium chloride	natural abundance		100 mM
9	D2O	natural abundance		100 %

12 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 10% C13-labeled

#	Name	Isotope labeling	Type	Concentration
10	GlUb(S27a)	[U-10% 13C]		1 mM
11	potassium phosphate	natural abundance		10 mM
12	sodium chloride	natural abundance		100 mM
13	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15547_2jx5.nef
Input source #2: Coordindates	2jx5.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---------
MLVIVRLQDQTLPFELPAGARASQLSNLLSSSGMAFSLHTQGRVLSEAAELNDKMVIDAFVPADGAGLE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MLVIVRLQDQTLPFELPAGARASQLSNLLSSSGMAFSLHTQGRVLSEAAELNDKMVIDAFVPADGAGLE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0

Content subtype: combined_15547_2jx5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	691		100.0 (chain: A, length: 69)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	1005 (1)	noe	100.0 (chain: A, length: 69)
2	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	48 (1)	hbond	43.5 (chain: A, length: 69)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	84 (84)	.	78.3 (chain: A, length: 69)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 360
  - ¹³C chemical shifts: 265
  - ¹⁵N chemical shifts: 66
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
- Total number of restraints: 1005
- Weight of restraints: 1.0 (1005)
- Potential type of restraints: upper-bound-parabolic (1005)
- Range of distance target values: 2.4, 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
- Saveframe: DYANA/DIANA_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 43.5%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: upper-bound-parabolic (48)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 78.3%
- Total number of restraints: 84
- Total number of restraints per polymer type: 84
- Weight of restraints: 1.0 (84)
- Potential type of restraints: square-well-parabolic (84)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords evolution, GlUb, recombination, ribosome, ubiquitin