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Found 1 Document (0.601 seconds)

BMRB: 16887

2K4E

Backbone 1H, 13C, 15N Chemical Shift Assignments for HIV-2 unmyristoylated matrix protein

Authors

Saad, J.S., Ablan, S.D., Ghanam, R.H., Kim, A., Andrews, K., Nagashima, K., Freed, E.O., Summers, M.F.

Assembly

HIV-2 unmyristoylated matrix protein

Entity

1. HIV-2 unmyristoylated matrix protein (polymer, Thiol state: all free), 134 monomers, 14871.02 Da Detail

GARNSVLRGK KADELERIRL RPGGKKKYRL KHIVWAANKL DRFGLAESLL ESKEGCQKIL TVLDPMVPTG SENLKSLFNT VCVIWCIHAE EKVKDTEGAK QIVRRHLVAE TGTAEKMPST SRPTAPSSEK GGNY

Formula weight

14871.02 Da

Source organism

Human immunodeficiency virus 2

Exptl. method

solution NMR

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 74.0 %, Completeness (bb): 77.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.0 % (1156 of 1563)	74.8 % (616 of 823)	68.3 % (412 of 603)	93.4 % (128 of 137)
Backbone	77.4 % (613 of 792)	90.1 % (246 of 273)	62.4 % (244 of 391)	96.1 % (123 of 128)
Sidechain	72.7 % (650 of 894)	67.3 % (370 of 550)	82.1 % (275 of 335)	55.6 % (5 of 9)
Aromatic	52.8 % (38 of 72)	52.8 % (19 of 36)	50.0 % (17 of 34)	100.0 % (2 of 2)
Methyl	92.6 % (137 of 148)	93.2 % (69 of 74)	91.9 % (68 of 74)

1. HIV2

GARNSVLRGK KADELERIRL RPGGKKKYRL KHIVWAANKL DRFGLAESLL ESKEGCQKIL TVLDPMVPTG SENLKSLFNT VCVIWCIHAE EKVKDTEGAK QIVRRHLVAE TGTAEKMPST SRPTAPSSEK GGNY

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	HIV-2 unmyristoylated matrix protein	[U-15N]	0.8 mM
2	potassium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	Glutamate	natural abundance	50 mM
5	Aspartate	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
9	HIV-2 unmyristoylated matrix protein	natural abundance	0.8 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	10 mM
12	Glutamate	natural abundance	50 mM
13	Aspartate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
16	HIV-2 unmyristoylated matrix protein	[U-13C; U-15N]	0.8 mM
17	potassium phosphate	natural abundance	20 mM
18	DTT	natural abundance	10 mM
19	Glutamate	natural abundance	50 mM
20	Aspartate	natural abundance	50 mM
21	sodium chloride	natural abundance	100 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	direct	1.0
¹H	water	protons	4.706 ppm	na	direct	1.0
¹⁵N	urea	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: 2.56 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	direct	1.0
¹H	water	protons	4.706 ppm	na	direct	1.0
¹⁵N	urea	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: 2.56 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl carbons	0.0 ppm	na	direct	1.0
¹H	water	protons	4.706 ppm	na	direct	1.0
¹⁵N	urea	nitrogen	0.0 ppm	na	direct	1.0

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4E, Strand ID: A Detail

Release date

2010-08-11

Citation

Structure of the myristylated human immunodeficiency virus type 2 matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in membrane targeting
Saad, J.S., Ablan, S.D., Ghanam, R.H., Kim, A., Andrews, K., Nagashima, K., Soheilian, F., Freed, E.O., Summers, M.F.
J. Mol. Biol. (2008), 382, 434-447, PubMed 18657545 , DOI 10.1016/j.jmb.2008.07.027 , Abstract

Related entities 1. HIV-2 unmyristoylated matrix protein, : 1 : 4 : 83 entities Detail

Interaction partners 1. HIV-2 unmyristoylated matrix protein, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	HIV-2 unmyristoylated matrix protein	[U-15N]	0.8 mM
2	potassium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	Glutamate	natural abundance	50 mM
5	Aspartate	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	HIV-2 unmyristoylated matrix protein	[U-15N]	0.8 mM
2	potassium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	Glutamate	natural abundance	50 mM
5	Aspartate	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 2D 1H-1H NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
9	HIV-2 unmyristoylated matrix protein	natural abundance	0.8 mM
10	potassium phosphate	natural abundance	20 mM
11	DTT	natural abundance	10 mM
12	Glutamate	natural abundance	50 mM
13	Aspartate	natural abundance	50 mM
14	sodium chloride	natural abundance	100 mM
15	D2O	natural abundance	100 %

4 3D HNCA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
16	HIV-2 unmyristoylated matrix protein	[U-13C; U-15N]	0.8 mM
17	potassium phosphate	natural abundance	20 mM
18	DTT	natural abundance	10 mM
19	Glutamate	natural abundance	50 mM
20	Aspartate	natural abundance	50 mM
21	sodium chloride	natural abundance	100 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

5 3D HN(CO)CA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
16	HIV-2 unmyristoylated matrix protein	[U-13C; U-15N]	0.8 mM
17	potassium phosphate	natural abundance	20 mM
18	DTT	natural abundance	10 mM
19	Glutamate	natural abundance	50 mM
20	Aspartate	natural abundance	50 mM
21	sodium chloride	natural abundance	100 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

6 3D 1H-15N TOCSY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	HIV-2 unmyristoylated matrix protein	[U-15N]	0.8 mM
2	potassium phosphate	natural abundance	20 mM
3	DTT	natural abundance	10 mM
4	Glutamate	natural abundance	50 mM
5	Aspartate	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16887_2k4e.nef
Input source #2: Coordindates	2k4e.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-
GARNSVLRGKKADELERIRLRPGGKKKYRLKHIVWAANKLDRFGLAESLLESKEGCQKILTVLDPMVPTGSENLKSLFNTVCVIWCIHAEEKVKDTEGAK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GARNSVLRGKKADELERIRLRPGGKKKYRLKHIVWAANKLDRFGLAESLLESKEGCQKILTVLDPMVPTGSENLKSLFNTVCVIWCIHAEEKVKDTEGAK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------110-------120-------130-----
QIVRRHLVAETGTAEKMPSTSRPTAPSSEKGGNY
||||||||||||||||||||||||||||||||||
QIVRRHLVAETGTAEKMPSTSRPTAPSSEKGGNY
-------110-------120-------130----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0

Content subtype: combined_16887_2k4e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1099		94.0 (chain: A, length: 134)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	964 (1)	noe	83.6 (chain: A, length: 134)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	16 (1)	hbond	11.2 (chain: A, length: 134)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 94.0%
- Total number of assignments
  - ¹H chemical shifts: 593
  - ¹⁵N chemical shifts: 126
  - ¹³C chemical shifts: 380
- 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	823	593	72.1
¹⁵N chemical shifts	147	126	85.7
¹³C chemical shifts	603	380	63.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	273	243	89.0
¹⁵N chemical shifts	128	121	94.5
¹³C chemical shifts	268	112	41.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	550	350	63.6
¹⁵N chemical shifts	19	5	26.3
¹³C chemical shifts	335	268	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	72	94.7
¹³C chemical shifts	76	71	93.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	19	52.8
¹⁵N chemical shifts	2	2	100.0
¹³C chemical shifts	34	17	50.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 83.6%
- Total number of restraints: 964
- Weight of restraints: 1.0 (964)
- Potential type of restraints: upper-bound-parabolic (964)
- Range of distance target values: 2.7, 5.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 11.2%
  - Total number of restraints: 16
  - Weight of restraints: 1.0 (16)
  - Potential type of restraints: upper-bound-parabolic (16)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords Protein

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Found 1 Document (0.601 seconds)

BMRB: 16887

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HIV-2 unmyristoylated matrix protein, : 1 : 4 : 83 entities Detail

Interaction partners 1. HIV-2 unmyristoylated matrix protein, : 1 interactors Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail