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BMRB: 25036

2MQJ

Solution structure of CsUbl

Authors

Assembly

CsUbl

Entity

1. CsUbl (polymer, Thiol state: all free), 88 monomers, 9243.753 Da Detail

HMKIKIVPAV GGGSPLELEV APNATVGAVR TKVCAMKKLP PDTTRLTYKG RALKDTETLE SLGVADGDKF VLITRTVGGC GEPIRRAA

Formula weight

9243.753 Da

Source organism

Candidatus Caldarchaeum subterraneum

Exptl. method

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 74.6 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.6 % (724 of 971)	76.1 % (383 of 503)	67.8 % (261 of 385)	96.4 % (80 of 83)
Backbone	81.8 % (422 of 516)	92.8 % (167 of 180)	68.9 % (175 of 254)	97.6 % (80 of 82)
Sidechain	70.9 % (378 of 533)	66.9 % (216 of 323)	77.5 % (162 of 209)	0.0 % (0 of 1)
Aromatic	0.0 % (0 of 22)	0.0 % (0 of 11)	0.0 % (0 of 11)
Methyl	79.2 % (95 of 120)	80.0 % (48 of 60)	78.3 % (47 of 60)

1. entity

HMKIKIVPAV GGGSPLELEV APNATVGAVR TKVCAMKKLP PDTTRLTYKG RALKDTETLE SLGVADGDKF VLITRTVGGC GEPIRRAA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 15N]		0.8 mM
6	sodium phosphate	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.07 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 0.07 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-06-21

Citation

Solution structure of ubiquitin-like protein from Caldiarchaeum subterraneum
Ye, K.
Not known

Related entities 1. CsUbl, : 1 : 4 : 124 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 15N]		0.8 mM
6	sodium phosphate	natural abundance		1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D C(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HBHA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.8 mM
2	sodium phosphate	natural abundance		1 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25036_2mqj.nef
Input source #2: Coordindates	2mqj.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--------80--------90-----
HMKIKIVPAVGGGSPLELEVAPNATVGAVRTKVCAMKKLPPDTTRLTYKGRALKDTETLESLGVADGDKFVLITRTVGGCGEPIRRAA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HMKIKIVPAVGGGSPLELEVAPNATVGAVRTKVCAMKKLPPDTTRLTYKGRALKDTETLESLGVADGDKFVLITRTVGGCGEPIRRAA
--------10--------20--------30--------40--------50--------60--------70--------80--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	88	0	0	100.0

Content subtype: combined_25036_2mqj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	702		98.9 (chain: A, length: 88)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	779 (1)	noe	83.0 (chain: A, length: 88)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	30 (1)	hbond	22.7 (chain: A, length: 88)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	112 (112)	.	80.7 (chain: A, length: 88)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 378
  - ¹³C chemical shifts: 244
  - ¹⁵N chemical shifts: 80
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 83.0%
- Total number of restraints: 779
- Weight of restraints: 1.0 (779)
- Potential type of restraints: square-well-parabolic (779)
- Range of distance target values: 2.6, 4.15 (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: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 22.7%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - Range of distance target values: 2.0, 3.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 88, Sequence coverage: 80.7%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Caldiarchaeum subterraneum, solution structure, ubquitin-like protein