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Found 1 Document (0.957 seconds)

BMRB: 25016

2MQ6

Solution structure of Y125F mutant of eRF1 N-domain

Authors

Pillay, S., Li, Y., Wong, L., Pervushin, K.

Assembly

Y125F mutant of eRF1 N-domain

Entity

1. Y125F mutant of eRF1 N-domain (polymer, Thiol state: all free), 142 monomers, 15661.01 Da Detail

MADDPSAADR NVEIWKIKKL IKSLEAARGN GTSMISLIIP PKDQISRVAK MLADEFGTAS NIKSRVNRLS VLGAITSVQQ RLKLYNKVPP NGLVVYCGTI VTEEGKEKKV NIDFEPFKPI NTSLFLCDNK FHTEALTALL SD

Formula weight

15661.01 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 85.4 %, Completeness (bb): 84.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.4 % (1424 of 1667)	91.1 % (792 of 869)	74.6 % (485 of 650)	99.3 % (147 of 148)
Backbone	84.0 % (704 of 838)	97.2 % (276 of 284)	70.2 % (294 of 419)	99.3 % (134 of 135)
Sidechain	87.7 % (845 of 964)	88.2 % (516 of 585)	86.3 % (316 of 366)	100.0 % (13 of 13)
Aromatic	64.6 % (53 of 82)	61.0 % (25 of 41)	67.5 % (27 of 40)	100.0 % (1 of 1)
Methyl	99.5 % (181 of 182)	98.9 % (90 of 91)	100.0 % (91 of 91)

1. entity

MADDPSAADR NVEIWKIKKL IKSLEAARGN GTSMISLIIP PKDQISRVAK MLADEFGTAS NIKSRVNRLS VLGAITSVQQ RLKLYNKVPP NGLVVYCGTI VTEEGKEKKV NIDFEPFKPI NTSLFLCDNK FHTEALTALL SD

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Concentration
1	Y125F mutant of eRF1 N-domain	[U-99% 15N]	1 mM
2	MES	natural abundance	20 mM
3	potassium chloride	natural abundance	100 mM
4	DTT	natural abundance	2 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.47 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.47 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.27 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MQ6, Strand ID: A Detail

Release date

2015-06-14

Citation

Structural insights of eRF1 mutants and their correlation with stop codon recognition
Pillay, S., Li, Y., Wong, L., Pervushin, K.
ACS chemical biology

Related entities 1. Y125F mutant of eRF1 N-domain, : 1 : 16 : 93 entities Detail

Interaction partners 1. Y125F mutant of eRF1 N-domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 3 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25016_2mq6.nef
Input source #2: Coordindates	2mq6.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-------100
MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTI

-------110-------120-------130-------140--
VTEEGKEKKVNIDFEPFKPINTSLFLCDNKFHTEALTALLSD
||||||||||||||||||||||||||||||||||||||||||
VTEEGKEKKVNIDFEPFKPINTSLFLCDNKFHTEALTALLSD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	142	0	0	100.0

Content subtype: combined_25016_2mq6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1380		98.6 (chain: A, length: 142)
1	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	1582 (1)	noe	97.9 (chain: A, length: 142)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	72 (1)	hbond	70.4 (chain: A, length: 142)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	236 (236)	.	95.8 (chain: A, length: 142)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_3	OK	78 (78)	.	54.9 (chain: A, length: 142)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 793
  - ¹³C chemical shifts: 441
  - ¹⁵N chemical shifts: 146
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
77	SER	HG	4.536
96	TYR	HH	7.336
127	CYS	HG	1.046

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	869	790	90.9
¹³C chemical shifts	650	441	67.8
¹⁵N chemical shifts	154	146	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	284	280	98.6
¹³C chemical shifts	284	136	47.9
¹⁵N chemical shifts	135	133	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	585	510	87.2
¹³C chemical shifts	366	305	83.3
¹⁵N chemical shifts	19	13	68.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	91	96.8
¹³C chemical shifts	94	92	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	23	56.1
¹³C chemical shifts	40	23	57.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 97.9%
- Total number of restraints: 1582
- Weight of restraints: 1.0 (1582)
- Potential type of restraints: upper-bound-parabolic (1582)
- Range of distance target values: 2.38, 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
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 70.4%
  - Total number of restraints: 72
  - Weight of restraints: 1.0 (72)
  - Potential type of restraints: upper-bound-parabolic (72)
  - Range of distance target values: 2.3, 2.3 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 95.8%
- Total number of restraints: 236
- Total number of restraints per polymer type: 236
- Weight of restraints: 1.0 (236)
- Potential type of restraints: square-well-parabolic (236)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 54.9%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MADDPSAADRNVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTI
         | ||    || || |||| ||   || | |  ||||||||  ||| |||   | | ||| |||| | | ||| ||||||  |||| ||   
.........R.VE....KK.IK.LEAA.GN...MI.L.I..KDQISRVA..LAD.FGT...I.S.VNR.SVLG.I.S.QQR.KLYNKV..NGLV.YC...
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140--
VTEEGKEKKVNIDFEPFKPINTSLFLCDNKFHTEALTALLSD
| ||   ||| ||||    |||| |||||||           
V.EE...KKV.IDFE....INTS.FLCDNKF           
-------110-------120-------130-

Total number of restraints: 78
Potential type of restraints: undefined (78)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

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Found 1 Document (0.957 seconds)

BMRB: 25016

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Y125F mutant of eRF1 N-domain, : 1 : 16 : 93 entities Detail

Interaction partners 1. Y125F mutant of eRF1 N-domain, : 1 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail