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BMRB: 15683

2K1S

Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli, Northeast Structural Genomics Consortium Target ER553.

Authors

Ramelot, T.A., Zhao, L., Hamilton, K., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Assembly

YiaD

Entity

1. YiaD (polymer, Thiol state: not present), 149 monomers, 16033.80 Da Detail

YYMDVQEAKL RDKMRGTGVS VTRSGDNIIL NMPNNVTFDS SSATLKPAGA NTLTGVAMVL KEYPKTAVNV IGYTDSTGGH DLNMRLSQQR ADSVASALIT QGVDASRIRT QGLGPANPIA SNSTAEGKAQ NRRVEITLSP LLEHHHHHH

Formula weight

16033.8 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: 98.7 %, Completeness: 95.9 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.9 % (1564 of 1631)	96.4 % (811 of 841)	95.1 % (600 of 631)	96.2 % (153 of 159)
Backbone	96.7 % (853 of 882)	97.4 % (296 of 304)	96.1 % (418 of 435)	97.2 % (139 of 143)
Sidechain	93.7 % (830 of 886)	94.0 % (505 of 537)	93.4 % (311 of 333)	87.5 % (14 of 16)
Aromatic	57.1 % (40 of 70)	60.0 % (21 of 35)	54.3 % (19 of 35)
Methyl	100.0 % (174 of 174)	100.0 % (87 of 87)	100.0 % (87 of 87)

1. YiaD

YYMDVQEAKL RDKMRGTGVS VTRSGDNIIL NMPNNVTFDS SSATLKPAGA NTLTGVAMVL KEYPKTAVNV IGYTDSTGGH DLNMRLSQQR ADSVASALIT QGVDASRIRT QGLGPANPIA SNSTAEGKAQ NRRVEITLSP LLEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	entity	[U-5% 13C; U-100% 15N]	1.3 (±0.1) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	100 (±5.0) mM
10	calcium chloride	natural abundance	5 (±0.2) mM
11	DTT	natural abundance	10 (±0.5) mM
12	sodium azide	natural abundance	0.02 (±0.001) %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
13	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
14	MES	natural abundance	20 (±1.0) mM
15	sodium chloride	natural abundance	100 (±5.0) mM
16	calcium chloride	natural abundance	5 (±0.2) mM
17	DTT	natural abundance	10 (±0.5) mM
18	sodium azide	natural abundance	0.02 (±0.001) %

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: -0.1 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: -0.1 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: -0.09 ppm, Outliers: 3 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: -0.08 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K1S, Strand ID: A Detail

Release date

2008-03-18

Citation

Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium Target ER553
Ramelot, T.A., Zhao, L., Hamilton, K., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Related entities 1. YiaD, : 1 : 1 : 2 : 39 entities Detail

Interaction partners 1. YiaD, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

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

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	entity	[U-5% 13C; U-100% 15N]	1.3 (±0.1) mM
8	MES	natural abundance	20 (±1.0) mM
9	sodium chloride	natural abundance	100 (±5.0) mM
10	calcium chloride	natural abundance	5 (±0.2) mM
11	DTT	natural abundance	10 (±0.5) mM
12	sodium azide	natural abundance	0.02 (±0.001) %

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

5 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

6 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
13	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
14	MES	natural abundance	20 (±1.0) mM
15	sodium chloride	natural abundance	100 (±5.0) mM
16	calcium chloride	natural abundance	5 (±0.2) mM
17	DTT	natural abundance	10 (±0.5) mM
18	sodium azide	natural abundance	0.02 (±0.001) %

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

8 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

9 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

10 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

11 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

12 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

13 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

14 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

15 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

16 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

17 4D CC NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
13	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
14	MES	natural abundance	20 (±1.0) mM
15	sodium chloride	natural abundance	100 (±5.0) mM
16	calcium chloride	natural abundance	5 (±0.2) mM
17	DTT	natural abundance	10 (±0.5) mM
18	sodium azide	natural abundance	0.02 (±0.001) %

18 2D 1H-13C HSQC (arom no ct)

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	1.9 (±0.1) mM
2	MES	natural abundance	20 (±1.0) mM
3	sodium chloride	natural abundance	100 (±5.0) mM
4	calcium chloride	natural abundance	5 (±0.2) mM
5	DTT	natural abundance	10 (±0.5) mM
6	sodium azide	natural abundance	0.02 (±0.001) %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15683_2k1s.nef
Input source #2: Coordindates	2k1s.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
YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YYMDVQEAKLRDKMRGTGVSVTRSGDNIILNMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQRADSVASALIT

-------110-------120-------130-------140---------
QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||
QGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITLSPLLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	149	0	0	100.0

Content subtype: combined_15683_2k1s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1571		98.0 (chain: A, length: 149)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1490 (1)	noe	96.0 (chain: A, length: 149)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	110 (1)	hbond	49.7 (chain: A, length: 149)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	198 (198)	.	81.9 (chain: A, length: 149)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 814
  - ¹³C chemical shifts: 596
  - ¹⁵N chemical shifts: 161
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
17	THR	HG1	6.01
52	THR	HG1	5.52
54	THR	HG1	5.26
66	THR	HG1	6.36
124	THR	HG1	5.69

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	841	809	96.2
¹³C chemical shifts	631	596	94.5
¹⁵N chemical shifts	168	161	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	304	296	97.4
¹³C chemical shifts	298	282	94.6
¹⁵N chemical shifts	143	138	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	537	513	95.5
¹³C chemical shifts	333	314	94.3
¹⁵N chemical shifts	25	23	92.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	92	92	100.0
¹³C chemical shifts	92	92	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	21	60.0
¹³C chemical shifts	35	19	54.3

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 96.0%
- Total number of restraints: 1489
- Weight of restraints: 1.0 (1489)
- Potential type of restraints: square-well-parabolic (1489)
- Range of distance target values: 2.35, 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_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 49.7%
  - Total number of restraints: 110
  - Weight of restraints: 1.0 (110)
  - Potential type of restraints: square-well-parabolic (110)
  - Range of distance target values: 1.9, 2.85 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 81.9%
- Total number of restraints: 198
- Total number of restraints per polymer type: 198
- Weight of restraints: 1.0 (198)
- Potential type of restraints: square-well-parabolic (198)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords abbababab, alpha beta, lipoprotein, OmpA

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Found 1 Document (0.733 seconds)

BMRB: 15683

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. YiaD, : 1 : 1 : 2 : 39 entities Detail

Interaction partners 1. YiaD, : 2 interactors Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 5 contents Detail