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BMRB: 25213

4UZW

HIGH-RESOLUTION NMR STRUCTURES OF THE DOMAINS OF SACCHAROMYCES CEREVISIAE THO1

Authors

Jacobsen, J.O.B., Allen, M.D., Freund, S.M.V., Bycroft, M.

Assembly

High-resolution NMR structures of the domains of Saccheromyces cerevisiae Tho1

Entity

1. High-resolution NMR structures of the domains of Saccheromyces cerevisiae Tho1 (polymer, Thiol state: not present), 50 monomers, 5518.103 Da Detail

SADYSSLTVV QLKDLLTKRN LSVGGLKNEL VQRLIKDDEE SKGESEVSPQ

Formula weight

5518.103 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.5 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.5 % (508 of 574)	94.7 % (285 of 301)	79.9 % (175 of 219)	88.9 % (48 of 54)
Backbone	96.3 % (287 of 298)	94.1 % (96 of 102)	97.3 % (143 of 147)	98.0 % (48 of 49)
Sidechain	83.0 % (268 of 323)	95.0 % (189 of 199)	66.4 % (79 of 119)	0.0 % (0 of 5)
Aromatic	50.0 % (4 of 8)	100.0 % (4 of 4)	0.0 % (0 of 4)
Methyl	100.0 % (62 of 62)	100.0 % (31 of 31)	100.0 % (31 of 31)

1. PROTEIN THO1

SADYSSLTVV QLKDLLTKRN LSVGGLKNEL VQRLIKDDEE SKGESEVSPQ

Show sample condition

Sample

Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

LACS Plot; CA

Referencing offset: -0.62 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.62 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.88 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 4UZW, Strand ID: A Detail

Release date

2014-12-14

Citation

High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1
Jacobsen, J.O.B., Allen, M.D., Freund, S.M.V., Bycroft, M.
Acta Crystallogr. F. Struct. Biol. Commun. (2016), 72, 500-506, PubMed 27303905 , DOI 10.1107/S2053230X16007597 , Abstract

Related entities 1. High-resolution NMR structures of the domains of Saccheromyces cerevisiae Tho1, : 1 : 1 : 3 : 27 entities Detail

Interaction partners 1. High-resolution NMR structures of the domains of Saccheromyces cerevisiae Tho1, : 12 interactors Detail

More details for 12 interactors identified by 4 citations

Experiments performed 10 experiments Detail

1 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

2 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

3 HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

4 CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

5 HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

6 HN(CA)CO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

7 HNHB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

8 1H-NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

9 1H-DQF-COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

10 1H-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% water/5% D2O, Pressure 1.000 atm, Temperature 293.000 K, pH 6.500, Details 1.5 mmol/l

#	Name	Isotope labeling	Type	Concentration
1	PROTEIN THO1	[U-13C; U-15N]		1.5 mM
2	potassium phosphate	natural abundance		20 mM
3	NaCl	natural abundance		100 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25213_4uzw.nef
Input source #2: Coordindates	4uzw.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
SADYSSLTVVQLKDLLTKRNLSVGGLKNELVQRLIKDDEESKGESEVSPQ
||||||||||||||||||||||||||||||||||||||||||||||||||
SADYSSLTVVQLKDLLTKRNLSVGGLKNELVQRLIKDDEESKGESEVSPQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	50	0	0	100.0

Content subtype: combined_25213_4uzw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	527		100.0 (chain: A, length: 50)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1668 (1)	noe	100.0 (chain: A, length: 50)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	48 (1)	hbond	60.0 (chain: A, length: 50)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	78 (78)	.	86.0 (chain: A, length: 50)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	19 (19)	.	38.0 (chain: A, length: 50)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 304
  - ¹³C chemical shifts: 175
  - ¹⁵N chemical shifts: 48
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 100.0%
- Total number of restraints: 1650
- Weight of restraints: 1.0 (1650)
- Potential type of restraints: square-well-parabolic (1650)
- Range of distance target values: 2.3, 3.9 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 60.0%
  - Total number of restraints: 48
  - Weight of restraints: 1.0 (48)
  - Potential type of restraints: square-well-parabolic (48)
  - Range of distance target values: 1.95, 2.9 (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: 50, Sequence coverage: 86.0%
- Total number of restraints: 78
- Total number of restraints per polymer type: 78
- Weight of restraints: 1.0 (78)
- Potential type of restraints: square-well-parabolic (78)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 50, Sequence coverage: 38.0%
  - Total number of restraints: 19
  - Total number of restraints per polymer type: 19
  - Weight of restraints: 1.0 (19)
  - Potential type of restraints: square-well-parabolic (19)
  - Dihedral angle restraints per residue

Keywords SAP, RNA BINDING PROTEIN