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Found 1 Document (0.681 seconds)

BMRB: 26022

2NCH

Solution structure of translation initiation factor IF1 from wolbachia endosymbiont strain TRS of Brugia malayi

Authors

Kabra, A., Nag, J., Arora, A., Bhattacharya, S.MISRA.

Assembly

translation initiation factor IF1

Entity

1. translation initiation factor IF1 (polymer), 87 monomers, 9934.576 Da Detail

MVKDEKSKTL FEVEGAVTAL LPAAEFRVKL DNEHEIICHV SGKVRRSKIR IIIGDRVLVE MSIYDRNAKK GRIIRRLKGT SDRTISK

Formula weight

9934.576 Da

Source organism

Wolbachia

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.5 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (953 of 1042)	90.7 % (498 of 549)	91.9 % (372 of 405)	94.3 % (83 of 88)
Backbone	97.5 % (507 of 520)	96.1 % (171 of 178)	98.8 % (253 of 256)	96.5 % (83 of 86)
Sidechain	87.3 % (527 of 604)	88.1 % (327 of 371)	86.6 % (200 of 231)	0.0 % (0 of 2)
Aromatic	33.3 % (12 of 36)	66.7 % (12 of 18)	0.0 % (0 of 18)
Methyl	95.6 % (109 of 114)	96.5 % (55 of 57)	94.7 % (54 of 57)

1. IF1

MVKDEKSKTL FEVEGAVTAL LPAAEFRVKL DNEHEIICHV SGKVRRSKIR IIIGDRVLVE MSIYDRNAKK GRIIRRLKGT SDRTISK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	IF1	[U-100% 15N]	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	PMSF	natural abundance	2 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	IF1	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	50 mM
14	sodium azide	natural abundance	0.1 %
15	PMSF	natural abundance	2 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.29 ppm, Outliers: 5 Detail

Protein Blocks Logo

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

Release date

2016-07-06

Citation

Solution structure of translation initiation factor IF1 from wolbachia endosymbiont strain TRS of Brugia malayi
Kabra, A., Nag, J., Arora, A., Bhattacharya, S.MISRA.
Not known

Related entities 1. translation initiation factor IF1, : 1 : 92 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	IF1	[U-100% 15N]	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	PMSF	natural abundance	2 mM

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

5 3D HN(CA)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

6 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	IF1	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	50 mM
14	sodium azide	natural abundance	0.1 %
15	PMSF	natural abundance	2 mM

7 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	IF1	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	50 mM
14	sodium azide	natural abundance	0.1 %
15	PMSF	natural abundance	2 mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	IF1	[U-100% 15N]	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	PMSF	natural abundance	2 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	IF1	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	50 mM
14	sodium azide	natural abundance	0.1 %
15	PMSF	natural abundance	2 mM

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	IF1	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	50 mM
14	sodium azide	natural abundance	0.1 %
15	PMSF	natural abundance	2 mM

11 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	IF1	[U-100% 15N]	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	PMSF	natural abundance	2 mM

12 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

13 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	IF1	[U-100% 13C; U-100% 15N]	0.8 ~ 1.0 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	sodium azide	natural abundance	0.1 %
10	PMSF	natural abundance	2 mM

14 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
11	IF1	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	20 mM
13	sodium chloride	natural abundance	50 mM
14	sodium azide	natural abundance	0.1 %
15	PMSF	natural abundance	2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_26022_2nch.nef
Input source #2: Coordindates	2nch.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-------
MVKDEKSKTLFEVEGAVTALLPAAEFRVKLDNEHEIICHVSGKVRRSKIRIIIGDRVLVEMSIYDRNAKKGRIIRRLKGTSDRTISK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVKDEKSKTLFEVEGAVTALLPAAEFRVKLDNEHEIICHVSGKVRRSKIRIIIGDRVLVEMSIYDRNAKKGRIIRRLKGTSDRTISK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_26022_2nch.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	Chemical_shifts	Warning	968		100.0 (chain: A, length: 87)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	1743 (1)	noe	100.0 (chain: A, length: 87)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	55 (1)	hbond	36.8 (chain: A, length: 87)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	126 (126)	.	90.8 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: Chemical_shifts
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 509
  - ¹³C chemical shifts: 376
  - ¹⁵N chemical shifts: 83
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
39	HIS	HD1	10.28

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	549	507	92.3
¹³C chemical shifts	405	376	92.8
¹⁵N chemical shifts	98	83	84.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	178	174	97.8
¹³C chemical shifts	174	174	100.0
¹⁵N chemical shifts	86	83	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	371	333	89.8
¹³C chemical shifts	231	202	87.4
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	55	93.2
¹³C chemical shifts	59	54	91.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	12	66.7
¹³C chemical shifts	18	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 100.0%
- Total number of restraints: 1743
- Weight of restraints: 1.0 (1743)
- Potential type of restraints: upper-bound-parabolic (1743)
- Range of distance target values: 2.06, 6.78 (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: 87, Sequence coverage: 36.8%
  - Total number of restraints: 55
  - Weight of restraints: 1.0 (55)
  - Potential type of restraints: upper-bound-parabolic (55)
  - Range of distance target values: 2.5, 3.5 (Å)
  - Histogram of distance target values
  - 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: 87, Sequence coverage: 90.8%
- Total number of restraints: 126
- Total number of restraints per polymer type: 126
- Weight of restraints: 1.0 (126)
- Potential type of restraints: square-well-parabolic (126)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.681 seconds)

BMRB: 26022

Sample #1

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. translation initiation factor IF1, : 1 : 92 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 5 contents Detail