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Found 1 Document (1.277 seconds)

BMRB: 15356

2JS7

Solution NMR Structure of Human Myeloid Differentiation Primary Response (MyD88). Northeast Structural Genomics target HR2869A.

Authors

Rossi, P., Ramelot, T.A., Ciano, M., Ho, C., Ma, L., Xiao, R., Acton, T.B., Kennedy, M.A., Tong, L., Montelione, G.T.

Assembly

HR2869A

Entity

1. HR2869A (polymer, Thiol state: all free), 160 monomers, 18730.62 Da Detail

MGITTLDDPL GHMPERFDAF ICYCPSDIQF VQEMIRQLEQ TNYRLKLCVS DRDVLPGTCV WSIASELIEK RCRRMVVVVS DDYLQSKECD FQTKFALSLS PGAHQKRLIP IKYKAMKKEF PSILRFITVC DYTNPCTKSW FWTRLAKALS LPLEHHHHHH

Formula weight

18730.62 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 93.4 %, Completeness (bb): 92.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.4 % (1818 of 1947)	94.6 % (961 of 1016)	92.3 % (709 of 768)	90.8 % (148 of 163)
Backbone	92.1 % (868 of 942)	93.7 % (295 of 315)	91.8 % (437 of 476)	90.1 % (136 of 151)
Sidechain	94.6 % (1098 of 1161)	95.0 % (666 of 701)	93.8 % (420 of 448)	100.0 % (12 of 12)
Aromatic	80.9 % (152 of 188)	80.9 % (76 of 94)	80.2 % (73 of 91)	100.0 % (3 of 3)
Methyl	100.0 % (172 of 172)	100.0 % (86 of 86)	100.0 % (86 of 86)

1. HR2869A

MGITTLDDPL GHMPERFDAF ICYCPSDIQF VQEMIRQLEQ TNYRLKLCVS DRDVLPGTCV WSIASELIEK RCRRMVVVVS DDYLQSKECD FQTKFALSLS PGAHQKRLIP IKYKAMKKEF PSILRFITVC DYTNPCTKSW FWTRLAKALS LPLEHHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0, Details Sample 1 liophylized and resuspended pH matched to starting sample by deuterated Acetic Acid

#	Name	Isotope labeling	Concentration
5	entity	[U-100% 13C; U-100% 15N]	0.8 mM
6	DTT	natural abundance	10 mM
7	ammonium acetate	natural abundance	40 mM
8	acetonitrile	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.8 mM
10	DTT	natural abundance	10 mM
11	ammonium acetate	natural abundance	40 mM
12	acetonitrile	natural abundance	5 %

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: -0.19 ppm, Outliers: 1 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: -0.19 ppm, Outliers: 1 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: -0.06 ppm, Outliers: 1 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: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JS7, Strand ID: A Detail

Release date

2007-07-23

Citation

Solution NMR Structure of Human Myeloid Differentiation Primary Response (MyD88). Northeast Structural Genomics target HR2869A
Rossi, P., Xiao, R., Acton, T.B., Tong, L., Montelione, G.T.
Not known

Related entities 1. HR2869A, : 1 : 11 : 111 entities Detail

Interaction partners 1. HR2869A, : 43 interactors Detail

More details for 43 interactors identified by 17 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

5 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

6 3D HNCOCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

12 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

14 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	entity	[U-5% 13C; U-100% 15N]	0.8 mM
2	DTT	natural abundance	10 mM
3	ammonium acetate	natural abundance	40 mM
4	acetonitrile	natural abundance	5 %

15 2D 1H-13C HSQC stereospecific VL

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.8 mM
10	DTT	natural abundance	10 mM
11	ammonium acetate	natural abundance	40 mM
12	acetonitrile	natural abundance	5 %

16 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0, Details Sample 1 liophylized and resuspended pH matched to starting sample by deuterated Acetic Acid

#	Name	Isotope labeling	Concentration
5	entity	[U-100% 13C; U-100% 15N]	0.8 mM
6	DTT	natural abundance	10 mM
7	ammonium acetate	natural abundance	40 mM
8	acetonitrile	natural abundance	5 %

17 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
5	entity	[U-100% 13C; U-100% 15N]	0.8 mM
6	DTT	natural abundance	10 mM
7	ammonium acetate	natural abundance	40 mM
8	acetonitrile	natural abundance	5 %

18 H/D exch

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
5	entity	[U-100% 13C; U-100% 15N]	0.8 mM
6	DTT	natural abundance	10 mM
7	ammonium acetate	natural abundance	40 mM
8	acetonitrile	natural abundance	5 %

19 HETnoe

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.8 mM
10	DTT	natural abundance	10 mM
11	ammonium acetate	natural abundance	40 mM
12	acetonitrile	natural abundance	5 %

20 T1/T2

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 5.0

#	Name	Isotope labeling	Concentration
9	entity	[U-100% 13C; U-100% 15N]	0.8 mM
10	DTT	natural abundance	10 mM
11	ammonium acetate	natural abundance	40 mM
12	acetonitrile	natural abundance	5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15356_2js7.nef
Input source #2: Coordindates	2js7.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:48:CYS:SG	A:72:CYS:SG	reduced, CA 54.722, CB 32.37 ppm	reduced, CA 57.335, CB 28.95 ppm	2.903

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
MGITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKECDFQTKFALSLS

-------110-------120-------130-------140-------150-------160
PGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAKALSLPLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAKALSLPLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	160	0	0	100.0

Content subtype: combined_15356_2js7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1823		96.3 (chain: A, length: 160)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3641 (1)	noe	94.4 (chain: A, length: 160)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 160, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 960
  - ¹³C chemical shifts: 708
  - ¹⁵N chemical shifts: 155
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1016	960	94.5
¹³C chemical shifts	768	708	92.2
¹⁵N chemical shifts	173	155	89.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	315	294	93.3
¹³C chemical shifts	320	288	90.0
¹⁵N chemical shifts	151	133	88.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	701	666	95.0
¹³C chemical shifts	448	420	93.8
¹⁵N chemical shifts	22	22	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	91	90	98.9
¹³C chemical shifts	91	90	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	76	80.9
¹³C chemical shifts	91	73	80.2
¹⁵N chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 160, Sequence coverage: 94.4%
- Total number of restraints: 3633
- Weight of restraints: 1.0 (3633)
- Potential type of restraints: square-well-parabolic (3633)
- Range of distance target values: 2.27, 3.85 (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

Keywords MyD88_HUMAN, NMR structure, TIR DOMAIN

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Found 1 Document (1.277 seconds)

BMRB: 15356

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HR2869A, : 1 : 11 : 111 entities Detail

Interaction partners 1. HR2869A, : 43 interactors Detail

Experiments performed 20 experiments Detail

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NMR combined restraints 3 contents Detail