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BMRB: 25214

4UZX

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), 67 monomers, 7488.387 Da Detail

GSALSPEEIK AKALDLLNKK LHRANKFGQD QADIDSLQRQ INRVEKFGVD LNSKLAEELG LVSRKNE

Formula weight

7488.387 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.9 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.9 % (730 of 794)	100.0 % (421 of 421)	81.5 % (243 of 298)	88.0 % (66 of 75)
Backbone	100.0 % (400 of 400)	100.0 % (137 of 137)	100.0 % (197 of 197)	100.0 % (66 of 66)
Sidechain	86.0 % (393 of 457)	100.0 % (284 of 284)	66.5 % (109 of 164)	0.0 % (0 of 9)
Aromatic	50.0 % (12 of 24)	100.0 % (12 of 12)	0.0 % (0 of 12)
Methyl	94.7 % (72 of 76)	100.0 % (38 of 38)	89.5 % (34 of 38)

1. PROTEIN THO1

GSALSPEEIK AKALDLLNKK LHRANKFGQD QADIDSLQRQ INRVEKFGVD LNSKLAEELG LVSRKNE

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: -0.77 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.77 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.92 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 4UZX, 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 : 2 : 14 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 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25214_4uzx.nef
Input source #2: Coordindates	4uzx.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

---120-----130-------140-------150-------160-------170-------180---
GSALSPEEIKAKALDLLNKKLHRANKFGQDQADIDSLQRQINRVEKFGVDLNSKLAEELGLVSRKNE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSALSPEEIKAKALDLLNKKLHRANKFGQDQADIDSLQRQINRVEKFGVDLNSKLAEELGLVSRKNE
--------10--------20--------30--------40--------50--------60-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	67	0	0	100.0

Content subtype: combined_25214_4uzx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	711		100.0 (chain: A, length: 67)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2147 (1)	noe	100.0 (chain: A, length: 67)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	64 (1)	hbond	64.2 (chain: A, length: 67)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	12 (12)	.	17.9 (chain: A, length: 67)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	110 (110)	.	92.5 (chain: A, length: 67)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	45 (45)	.	67.2 (chain: A, length: 67)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 420
  - ¹³C chemical shifts: 225
  - 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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 100.0%
- Total number of restraints: 2121
- Weight of restraints: 1.0 (2121)
- Potential type of restraints: square-well-parabolic (2121)
- 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: 67, Sequence coverage: 64.2%
  - Total number of restraints: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - 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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 17.9%
- Total number of restraints: 12
- Total number of restraints per polymer type: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: square-well-parabolic (12)
- Dihedral angle restraints per residue
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 92.5%
  - Total number of restraints: 110
  - Total number of restraints per polymer type: 110
  - Weight of restraints: 1.0 (110)
  - Potential type of restraints: square-well-parabolic (110)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 67.2%
- Total number of restraints: 45
- Potential type of restraints: undefined (45)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Tho1, RNA BINDING PROTEIN