BMRBj - BMREntryMaster

Found 1 Document (0.538 seconds)

BMRB: 12032

6OX7

Solution NMR structure of the W187R mutant of 1918 NS1 effector domain

Authors

Shen, Q., Cho, J.

Assembly

NS1 effector domain

Entity

1. NS1 effector domain (polymer, Thiol state: all free), 119 monomers, 13486.47 Da Detail

SRYLTDMTLE EMSRDWFMLM PKQKVAGSLC IRMDQAIMDK NIILKANFSV IFDRLETLIL LRAFTEEGAI VGEISPLPSL PGHTDEDVKN AVGVLIGGLE RNDNTVRVSE TLQRFAWRS

Formula weight

13486.47 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 87.1 %, Completeness (bb): 93.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.1 % (1220 of 1400)	86.5 % (629 of 727)	85.9 % (471 of 548)	96.0 % (120 of 125)
Backbone	93.9 % (663 of 706)	95.4 % (230 of 241)	92.0 % (322 of 350)	96.5 % (111 of 115)
Sidechain	81.8 % (659 of 806)	81.7 % (397 of 486)	81.6 % (253 of 310)	90.0 % (9 of 10)
Aromatic	68.6 % (59 of 86)	76.7 % (33 of 43)	58.5 % (24 of 41)	100.0 % (2 of 2)
Methyl	86.2 % (131 of 152)	84.2 % (64 of 76)	88.2 % (67 of 76)

1. NS1 effector domain

SRYLTDMTLE EMSRDWFMLM PKQKVAGSLC IRMDQAIMDK NIILKANFSV IFDRLETLIL LRAFTEEGAI VGEISPLPSL PGHTDEDVKN AVGVLIGGLE RNDNTVRVSE TLQRFAWRS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

Referencing offset: -0.14 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.14 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.12 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.35 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6NU0, Strand ID: A Detail

Release date

2019-02-02

Citation

The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus
Shen, Q., Cho, J.
Biochem. Biophys. Res. Commun. (2019), 518, 178-182, PubMed 31420169 , DOI 10.1016/j.bbrc.2019.08.027 , Abstract

Related entities 1. NS1 effector domain, : 1 : 1 : 4 : 129 entities Detail

Interaction partners 1. NS1 effector domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

6 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

8 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.2 mM
2	sodium phosphate	natural abundance	buffer	20 mM
3	sodium chloride	natural abundance	salt	80 mM
4	DTT	natural abundance		1 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.15 mM
8	sodium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	80 mM
10	DTT	natural abundance		1 mM
11	D2O	[U-2H]	solvent	100 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
7	NS1 effector domain	[U-98% 13C; U-98% 15N]	protein	0.1 ~ 0.15 mM
8	sodium phosphate	natural abundance	buffer	20 mM
9	sodium chloride	natural abundance	salt	80 mM
10	DTT	natural abundance		1 mM
11	D2O	[U-2H]	solvent	100 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr12032_3.str
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

Content subtype: bmr12032_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1352		97.5 (chain: 1, length: 119)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 119, Sequence coverage: 97.5%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
SRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNAVGVLIGGLE
|||||||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||
SRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMDQAIMDKNIILKANFSVIFDR.E.LILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNAVGVLIGGLE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110---------
RNDNTVRVSETLQRFAWRS
|||||||||||||||||| 
RNDNTVRVSETLQRFAWR 
-------110--------

Total number of assignments
- ¹H chemical shifts: 750
- ¹³C chemical shifts: 482
- ¹⁵N chemical shifts: 120

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	GLU	CD	189.205
11	GLU	CD	183.071
15	ASP	CG	182.162
23	GLN	CD	190.624
35	GLN	CD	182.715
39	ASP	CG	185.148
41	ASN	CG	182.638
47	ASN	CG	185.503
66	GLU	CD	189.718
67	GLU	CD	191.45
73	GLU	CD	189.808
85	ASP	CG	180.995
86	GLU	CD	189.413
87	ASP	CG	188.215
103	ASP	CG	185.938
110	GLU	CD	190.119

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	727	620	85.3
¹³C chemical shifts	548	466	85.0
¹⁵N chemical shifts	134	120	89.6

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	241	227	94.2
¹³C chemical shifts	238	214	89.9
¹⁵N chemical shifts	115	109	94.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	486	393	80.9
¹³C chemical shifts	310	252	81.3
¹⁵N chemical shifts	19	11	57.9

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	65	79.3
¹³C chemical shifts	82	68	82.9

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	33	76.7
¹³C chemical shifts	41	24	58.5
¹⁵N chemical shifts	2	2	100.0

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: 1