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Found 1 Document (0.739 seconds)

BMRB: 34106

5N9V

NMR solution structure of ubl5 domain from polyubiquitin locus of T.thermophila.

Authors

Chiarini, V., Tossavainen, H.

Assembly

NAD(P)(+)--arginine ADP-ribosyltransferase (E.C.2.4.2.31)

Entity

1. NAD(P)(+)--arginine ADP-ribosyltransferase (E.C.2.4.2.31) (polymer, Thiol state: not present), 81 monomers, 9444.743 Da Detail

SHMQVSIEFQ NGEKLKFNVQ PSHKILDIKE MIFKKTNINV KDQSLKFAGN EMINQKTLSD YSIIDSTEEF TLHLETKLDL M

Formula weight

9444.743 Da

Source organism

Tetrahymena thermophila SB210

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.0 %, Completeness (bb): 95.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.0 % (956 of 1006)	93.0 % (491 of 528)	97.2 % (376 of 387)	97.8 % (89 of 91)
Backbone	95.9 % (464 of 484)	91.4 % (149 of 163)	98.3 % (237 of 241)	97.5 % (78 of 80)
Sidechain	94.8 % (570 of 601)	93.7 % (342 of 365)	96.4 % (217 of 225)	100.0 % (11 of 11)
Aromatic	85.7 % (60 of 70)	85.7 % (30 of 35)	85.7 % (30 of 35)
Methyl	96.6 % (85 of 88)	97.7 % (43 of 44)	95.5 % (42 of 44)

1. entity 1

SHMQVSIEFQ NGEKLKFNVQ PSHKILDIKE MIFKKTNINV KDQSLKFAGN EMINQKTLSD YSIIDSTEEF TLHLETKLDL M

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 4 mM [U-13C; U-15N] T.thermophila BUBL1-ubl5, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	indirect	0.2514502
¹H	water	protons	4.64 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	indirect	0.2514502
¹H	water	protons	4.64 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	indirect	0.2514502
¹H	water	protons	4.64 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	indirect	0.2514502
¹H	water	protons	4.64 ppm	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5N9V, Strand ID: A Detail

Release date

2018-03-13

Citation

NMR structure of a non-conjugatable, ADP-ribosylation associated, ubiquitin-like domain from Tetrahymena thermophila polyubiquitin locus
Chiarini, V., Tossavainen, H., Sharma, V., Colotti, G.
Biochim. Biophys. Acta. Gen. Subj. (2019), 1863, 749-759, PubMed 30690122 , DOI 10.1016/j.bbagen.2019.01.014 , Abstract

Related entities 1. NAD(P)(+)--arginine ADP-ribosyltransferase (E.C.2.4.2.31), : 1 : 632 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 4 mM [U-13C; U-15N] T.thermophila BUBL1-ubl5, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

3 3D 1H-15N TOCSY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

4 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

5 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

6 3D HNCO

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

7 3D HNCACB

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

8 3D HNCA

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

9 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

10 3D HN(CO)CA

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

11 3D HN(CA)CO

Instrument

Bruker AvanceIII - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

12 3D HCC(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

13 3D HCCH-COSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	T.thermophila BUBL1-ubl5	[U-13C; U-15N]		4 mM
2	sodium phosphate	natural abundance		20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34106_5n9v.nef
Input source #2: Coordindates	5n9v.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-
SHMQVSIEFQNGEKLKFNVQPSHKILDIKEMIFKKTNINVKDQSLKFAGNEMINQKTLSDYSIIDSTEEFTLHLETKLDLM
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SHMQVSIEFQNGEKLKFNVQPSHKILDIKEMIFKKTNINVKDQSLKFAGNEMINQKTLSDYSIIDSTEEFTLHLETKLDLM

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	81	0	0	100.0

Content subtype: combined_34106_5n9v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1001		100.0 (chain: A, length: 81)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1672 (1)	noe	98.8 (chain: A, length: 81)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	125 (125)	.	88.9 (chain: A, length: 81)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 521
  - ¹³C chemical shifts: 391
  - ¹⁵N chemical shifts: 89
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
4	GLN	CD	180.733
10	GLN	CD	180.612
11	ASN	CG	176.918
18	ASN	CG	176.414
20	GLN	CD	180.1
37	ASN	CG	178.332
39	ASN	CG	175.992
43	GLN	CD	175.166
50	ASN	CG	176.516
54	ASN	CG	174.843
55	GLN	CD	180.638

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	528	521	98.7
¹³C chemical shifts	387	380	98.2
¹⁵N chemical shifts	91	89	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	163	161	98.8
¹³C chemical shifts	162	162	100.0
¹⁵N chemical shifts	80	78	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	365	360	98.6
¹³C chemical shifts	225	218	96.9
¹⁵N chemical shifts	11	11	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	48	100.0
¹³C chemical shifts	48	46	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	30	85.7
¹³C chemical shifts	35	30	85.7

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 98.8%
- Total number of restraints: 1672
- Weight of restraints: 1.0 (1672)
- Potential type of restraints: upper-bound-parabolic (1672)
- Range of distance target values: 2.33, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 81, Sequence coverage: 88.9%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ULD, beta-grasp, polyubiquitin, transferase

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Found 1 Document (0.739 seconds)

BMRB: 34106

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NAD(P)(+)--arginine ADP-ribosyltransferase (E.C.2.4.2.31), : 1 : 632 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail