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Found 1 Document (0.701 seconds)

BMRB: 15139

2JO6

NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100

Authors

Ramelot, T.A., Cort, J.R., Yee, A.A., Guido, V., Lukin, J.A., Arrowsmith, C.H., Kennedy, M.A.

Assembly

NirD

Entity

1. NirD (polymer, Thiol state: all free), 113 monomers, 12750.31 Da Detail

QGHMSQWKDI CKIDDILPET GVCALLGDEQ VAIFRPYHSD QVFAISNIDP FFESSVLSRG LIAEHQGELW VASPLKKQRF RLSDGLCMED EQFSVKHYEA RVKDGVVQLR GGS

Formula weight

12750.31 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 95.7 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.7 % (1266 of 1323)	96.5 % (665 of 689)	94.6 % (486 of 514)	95.8 % (115 of 120)
Backbone	95.7 % (641 of 670)	96.5 % (223 of 231)	94.8 % (313 of 330)	96.3 % (105 of 109)
Sidechain	96.0 % (727 of 757)	96.5 % (442 of 458)	95.5 % (275 of 288)	90.9 % (10 of 11)
Aromatic	87.1 % (101 of 116)	89.7 % (52 of 58)	83.9 % (47 of 56)	100.0 % (2 of 2)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. NirD

QGHMSQWKDI CKIDDILPET GVCALLGDEQ VAIFRPYHSD QVFAISNIDP FFESSVLSRG LIAEHQGELW VASPLKKQRF RLSDGLCMED EQFSVKHYEA RVKDGVVQLR GGS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
9	protein	[U-100% 13C]	1 (±0.2) mM
10	TRIS	natural abundance	10 (±1.0) mM
11	sodium chloride	natural abundance	300 (±5.0) mM
12	ZINC ION	natural abundance	10 (±1.0) uM
13	DTT	natural abundance	10 (±1.0) mM
14	sodium azide	natural abundance	0.01 (±0.001) %
15	D2O		100 %

LACS Plot; CA

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

Referencing offset: 0.15 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 0.15 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.75 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JO6, Strand ID: A Detail

Release date

2007-02-21

Citation

NMR structure of E.coli NirD
Ramelot, T.A., Cort, J.R., Yee, A.A., Arrowsmith, C.H., Kennedy, M.A.

Related entities 1. NirD, : 1 : 2 : 8 entities Detail

Experiments performed 10 experiments Detail

1 3D 1H-15N NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

2 2D 1H-15N HSQC (NH2 only)

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

3 2D 1H-13C HSQC (aliph)

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

5 3D 1H-13C NOESY (aliph)

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

6 4D CC NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
9	protein	[U-100% 13C]	1 (±0.2) mM
10	TRIS	natural abundance	10 (±1.0) mM
11	sodium chloride	natural abundance	300 (±5.0) mM
12	ZINC ION	natural abundance	10 (±1.0) uM
13	DTT	natural abundance	10 (±1.0) mM
14	sodium azide	natural abundance	0.01 (±0.001) %
15	D2O		100 %

7 3D 1H-13C NOESY (arom)

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

8 2D 1H-15N HSQC (open)

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

9 2D 1H-15N HSQC (optimized)

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

10 2D 1H-13C HSQC (arom ct)

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	300 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %
7	H2O		95 %
8	D2O		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15139_2jo6.nef
Input source #2: Coordindates	2jo6.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-------
QGHMSQWKDICKIDDILPETGVCALLGDEQVAIFRPYHSDQVFAISNIDPFFESSVLSRGLIAEHQGELWVASPLKKQRFRLSDGLCMEDEQFSVKHYEA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QGHMSQWKDICKIDDILPETGVCALLGDEQVAIFRPYHSDQVFAISNIDPFFESSVLSRGLIAEHQGELWVASPLKKQRFRLSDGLCMEDEQFSVKHYEA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

100-------110
RVKDGVVQLRGGS
|||||||||||||
RVKDGVVQLRGGS
-------110---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_15139_2jo6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1275		97.3 (chain: A, length: 113)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1145 (1)	noe	95.6 (chain: A, length: 113)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	69 (1)	hbond	23.0 (chain: A, length: 113)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	134 (134)	.	84.1 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 665
  - ¹³C chemical shifts: 491
  - ¹⁵N chemical shifts: 119
- 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)
3	GLN	CD	180.4
17	THR	HG1	6.46
32	ARG	HH11	6.01
32	ARG	HH12	6.01
32	ARG	NH1	67.6
38	GLN	CD	179.9
63	GLN	CD	180.7
78	ARG	HH11	6.68
78	ARG	HH12	6.68
78	ARG	NH1	72.4
89	GLN	CD	180.4
91	SER	HG	6.28
105	GLN	CD	178.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	689	659	95.6
¹³C chemical shifts	514	486	94.6
¹⁵N chemical shifts	126	117	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	231	220	95.2
¹³C chemical shifts	226	211	93.4
¹⁵N chemical shifts	109	102	93.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	458	439	95.9
¹³C chemical shifts	288	275	95.5
¹⁵N chemical shifts	17	15	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	60	98.4
¹³C chemical shifts	61	60	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	49	84.5
¹³C chemical shifts	56	47	83.9
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 95.6%
- Total number of restraints: 1143
- Weight of restraints: 1.0 (1143)
- Potential type of restraints: square-well-parabolic (1143)
- Range of distance target values: 2.15, 3.4 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 23.0%
  - Total number of restraints: 69
  - Weight of restraints: 1.0 (69)
  - Potential type of restraints: square-well-parabolic (69)
  - Range of distance target values: 2.0, 3.15 (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: 113, Sequence coverage: 84.1%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 3-layer sandwich, ISP domain, Rieske iron-sulfur protein, all beta

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Found 1 Document (0.701 seconds)

BMRB: 15139

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NirD, : 1 : 2 : 8 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail