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Found 1 Document (0.702 seconds)

BMRB: 19168

2M71

Solution structure of the a C-terminal domain of translation initiation factor IF-3 from Campylobacter jejuni

Authors

Love, J.D., Harris, R., Ahmed, M., Attonito, J., Bonanno, J.B., Chamala, S., Chowdhury, S., Evans, B., Fiser, A., Glenn, A.S., Hammonds, J., Hillerich, B., Khafizov, K., Lafleur, J., Seidel, R.D., Stead, M., Girvin, M.E., Almo, S.C.

Assembly

C-terminal domain of translation initiation factor IF-3

Entity

1. C-terminal domain of translation initiation factor IF-3 (polymer, Thiol state: not present), 101 monomers, 11808.56 Da Detail

MSLKVIDIKE IKLSVKIAQN DINYKVKHAL EFLEQGKHVR FRVFLKGREM ATPEAGVALL EKIWTMIENE ANRDKEPNFE GRYVNMLVTP KKAEGHHHHH H

Formula weight

11808.56 Da

Source organism

Campylobacter jejuni

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 90.7 %, Completeness (bb): 91.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.7 % (1130 of 1246)	90.2 % (591 of 655)	91.3 % (442 of 484)	90.7 % (97 of 107)
Backbone	91.5 % (549 of 600)	90.2 % (184 of 204)	93.0 % (277 of 298)	89.8 % (88 of 98)
Sidechain	90.4 % (671 of 742)	90.2 % (407 of 451)	90.4 % (255 of 282)	100.0 % (9 of 9)
Aromatic	72.0 % (72 of 100)	72.0 % (36 of 50)	71.4 % (35 of 49)	100.0 % (1 of 1)
Methyl	95.5 % (107 of 112)	94.6 % (53 of 56)	96.4 % (54 of 56)

1. IF-3

MSLKVIDIKE IKLSVKIAQN DINYKVKHAL EFLEQGKHVR FRVFLKGREM ATPEAGVALL EKIWTMIENE ANRDKEPNFE GRYVNMLVTP KKAEGHHHHH H

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate pH6.8, 50mM NaCl, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	IF-3	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	100 %
9	Na phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.1 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: 0.15 ppm, Outliers: 1 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: 0.15 ppm, Outliers: 1 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: -0.11 ppm, Outliers: 1 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: -0.09 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M71, Strand ID: A Detail

Release date

2013-05-01

Related entities 1. C-terminal domain of translation initiation factor IF-3, : 1 : 2 : 124 entities Detail

Interaction partners 1. C-terminal domain of translation initiation factor IF-3, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

3 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate pH6.8, 50mM NaCl, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	IF-3	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	100 %
9	Na phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.1 mM

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate pH6.8, 50mM NaCl, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	IF-3	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	100 %
9	Na phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.1 mM

5 13C NOESY-HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate pH6.8, 50mM NaCl, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	IF-3	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	100 %
9	Na phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.1 mM

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate pH6.8, 50mM NaCl, 0.1mM EDTA

#	Name	Isotope labeling	Concentration
7	IF-3	[U-100% 13C; U-100% 15N]	1 mM
8	D2O	natural abundance	100 %
9	Na phosphate buffer	natural abundance	20 mM
10	NaCl	natural abundance	50 mM
11	EDTA	natural abundance	0.1 mM

7 HNCO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

8 HNCACO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

9 HNCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

10 HNCOCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

11 HNCACB

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

12 CBCACONH

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 0.1 mM EDTA

#	Name	Isotope labeling	Concentration
1	IF-3	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	Na phosphate buffer	natural abundance	20 mM
5	NaCl	natural abundance	50 mM
6	EDTA	natural abundance	0.1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19168_2m71.nef
Input source #2: Coordindates	2m71.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
MSLKVIDIKEIKLSVKIAQNDINYKVKHALEFLEQGKHVRFRVFLKGREMATPEAGVALLEKIWTMIENEANRDKEPNFEGRYVNMLVTPKKAEGHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLKVIDIKEIKLSVKIAQNDINYKVKHALEFLEQGKHVRFRVFLKGREMATPEAGVALLEKIWTMIENEANRDKEPNFEGRYVNMLVTPKKAEGHHHHH

-
H
|
H

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0

Content subtype: combined_19168_2m71.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1117		91.1 (chain: A, length: 101)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1818 (1)	noe	91.1 (chain: A, length: 101)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	138 (1)	noe	57.4 (chain: A, length: 101)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	143 (143)	.	74.3 (chain: A, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 91.1%
- Total number of assignments
  - ¹H chemical shifts: 589
  - ¹³C chemical shifts: 433
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	655	589	89.9
¹³C chemical shifts	484	433	89.5
¹⁵N chemical shifts	112	95	84.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	204	181	88.7
¹³C chemical shifts	202	181	89.6
¹⁵N chemical shifts	98	84	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	451	408	90.5
¹³C chemical shifts	282	252	89.4
¹⁵N chemical shifts	14	11	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	57	95.0
¹³C chemical shifts	60	57	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	36	72.0
¹³C chemical shifts	49	35	71.4
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 91.1%
- Total number of restraints: 1814
- Weight of restraints: 1.0 (1814)
- Potential type of restraints: square-well-parabolic (1814)
- Range of distance target values: 2.4, 4.15 (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: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 57.4%
  - Total number of restraints: 138
  - Weight of restraints: 1.0 (138)
  - Potential type of restraints: square-well-parabolic (138)
  - Range of distance target values: 2.4, 3.9 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 74.3%
- Total number of restraints: 143
- Total number of restraints per polymer type: 143
- Weight of restraints: 1.0 (143)
- Potential type of restraints: square-well-parabolic (143)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords New York Structural Genomics Research Consortium, STRUCTURAL GENOMICS, TRANSLATION INITIATION FACTOR

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Found 1 Document (0.702 seconds)

BMRB: 19168

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. C-terminal domain of translation initiation factor IF-3, : 1 : 2 : 124 entities Detail

Interaction partners 1. C-terminal domain of translation initiation factor IF-3, : 1 interactors Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail