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BMRB: 19416

2MBY

NMR Structure of Rrp7 C-terminal Domain

Authors

Lin, J., Feng, Y., Ye, K.

Assembly

Rrp7 C-terminal Domain

Entity

1. Rrp7 C-terminal Domain (polymer, Thiol state: not present), 46 monomers, 5719.531 Da Detail

GPEADFYRFQ VRERKKQEIN QLLSKFKEDQ ERIKVMKAKR KFNPYT

Formula weight

5719.531 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.8 %, Completeness (bb): 99.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.8 % (590 of 616)	95.5 % (320 of 335)	95.2 % (220 of 231)	100.0 % (50 of 50)
Backbone	99.3 % (270 of 272)	97.8 % (89 of 91)	100.0 % (137 of 137)	100.0 % (44 of 44)
Sidechain	93.8 % (365 of 389)	94.7 % (231 of 244)	92.1 % (128 of 139)	100.0 % (6 of 6)
Aromatic	66.1 % (37 of 56)	71.4 % (20 of 28)	60.7 % (17 of 28)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 of 15)

1. entity

GPEADFYRFQ VRERKKQEIN QLLSKFKEDQ ERIKVMKAKR KFNPYT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

Protein Blocks Logo

Calculated from 1 models in PDB: 2MBY, Strand ID: A Detail

Release date

2013-09-22

Citation

An RNA-binding complex involved in ribosome biogenesis contains a protein with homology to tRNA CCA-adding enzyme
Lin, J., Lu, J., Feng, Y., Sun, M., Ye, K.
PLoS Biol. (2013), 11, e1001669-e1001669, PubMed 24130456 , DOI 10.1371/journal.pbio.1001669 , Abstract

Related entities 1. Rrp7 C-terminal Domain, : 1 : 6 : 31 entities Detail

Interaction partners 1. Rrp7 C-terminal Domain, : 43 interactors Detail

More details for 43 interactors identified by 10 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

2 3D 1H-15N TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

3 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

4 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

5 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

6 3D HN(CO)CA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

7 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

8 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

9 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

10 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

11 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	potassium phosphate	natural abundance		50 mM
3	sodium azide	natural abundance		0.05 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19416_2mby.nef
Input source #2: Coordindates	2mby.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

------260-------270-------280-------290-------
GPEADFYRFQVRERKKQEINQLLSKFKEDQERIKVMKAKRKFNPYT
||||||||||||||||||||||||||||||||||||||||||||||
GPEADFYRFQVRERKKQEINQLLSKFKEDQERIKVMKAKRKFNPYT
--------10--------20--------30--------40------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	46	0	0	100.0

Content subtype: combined_19416_2mby.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	585		97.8 (chain: A, length: 46)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	523 (1)	noe	97.8 (chain: A, length: 46)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	40 (1)	hbond	60.9 (chain: A, length: 46)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	68 (68)	.	87.0 (chain: A, length: 46)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 318
  - ¹³C chemical shifts: 218
  - ¹⁵N chemical shifts: 49
- 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: 46, Sequence coverage: 97.8%
- Total number of restraints: 523
- Weight of restraints: 1.0 (523)
- Potential type of restraints: square-well-parabolic (523)
- Range of distance target values: 2.3, 3.9 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 60.9%
  - Total number of restraints: 40
  - Weight of restraints: 1.0 (40)
  - Potential type of restraints: square-well-parabolic (40)
  - 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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 46, Sequence coverage: 87.0%
- Total number of restraints: 68
- Total number of restraints per polymer type: 68
- Weight of restraints: 1.0 (68)
- Potential type of restraints: square-well-parabolic (68)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Helix, Rrp7