BMRBj - BMREntryMaster

Found 1 Document (1.92 seconds)

BMRB: 4141

1NK2

vnd/NK-2 Homeodomain DNA Complex Protein 1H, 13C, and 15N Chemical Shifts and HNHA Coupling Constant

Authors

Gruschus, J.M., Tsao, D.H.H., Wang, L., Nirenberg, M., Ferretti, J.A.

Assembly

vnd/NK-2 homeodomain DNA complex

Entity

1. vnd/NK-2 homeodomain (polymer, Thiol state: not present), 77 monomers, 9352.561 Da Detail

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT (polymer, Thiol state: not present), 16 monomers, 5023.183 Da Detail

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA (polymer, Thiol state: not present), 17 monomers, 5212.350 Da Detail

ACAGCCACTT GACACAA

Total weight

19588.094 Da

Max. entity weight

9352.561 Da

Source organism

Drosophila melanogaster

Exptl. method

NMR

Refine. method

DISTANCE GEOMETRY/ SIMULATED ANNEALING

Data set

assigned_chemical_shifts, coupling_constants

Chem. Shift Complete1

Sequence coverage: 70.0 %, Completeness: 68.2 %, Completeness (bb): 53.6 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	68.2 % (912 of 1338)	62.0 % (527 of 850)	81.7 % (304 of 372)	97.6 % (81 of 83)	0.0 % (0 of 33)
Backbone	53.6 % (385 of 718)	39.6 % (152 of 384)	71.1 % (162 of 228)	97.3 % (71 of 73)	0.0 % (0 of 33)
Sidechain	86.6 % (601 of 694)	80.5 % (375 of 466)	99.1 % (216 of 218)	100.0 % (10 of 10)
Aromatic	56.6 % (86 of 152)	39.4 % (43 of 109)	100.0 % (42 of 42)	100.0 % (1 of 1)
Methyl	88.9 % (64 of 72)	80.0 % (32 of 40)	100.0 % (32 of 32)

1. vnd/NK-2 homeodomain

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA

ACAGCCACTT GACACAA

Show sample condition

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

Chem. Shift Complete2

Sequence coverage: 28.2 %, Completeness: 42.8 %, Completeness (bb): 38.2 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	42.8 % (1145 of 2676)	40.7 % (692 of 1700)	46.6 % (347 of 744)	56.6 % (94 of 166)	18.2 % (12 of 66)
Backbone	38.2 % (549 of 1436)	33.3 % (256 of 768)	43.2 % (197 of 456)	57.5 % (84 of 146)	18.2 % (12 of 66)
Sidechain	49.1 % (682 of 1388)	46.8 % (436 of 932)	54.1 % (236 of 436)	50.0 % (10 of 20)
Aromatic	38.2 % (116 of 304)	33.5 % (73 of 218)	50.0 % (42 of 84)	50.0 % (1 of 2)
Methyl	52.8 % (76 of 144)	51.2 % (41 of 80)	54.7 % (35 of 64)

1. vnd/NK-2 homeodomain

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA

ACAGCCACTT GACACAA

Show sample condition

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

Chem. Shift Complete3

Sequence coverage: 31.8 %, Completeness: 35.2 %, Completeness (bb): 33.1 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	35.2 % (1413 of 4014)	35.5 % (904 of 2550)	34.4 % (384 of 1116)	43.0 % (107 of 249)	18.2 % (18 of 99)
Backbone	33.1 % (714 of 2154)	32.0 % (369 of 1152)	33.6 % (230 of 684)	44.3 % (97 of 219)	18.2 % (18 of 99)
Sidechain	38.1 % (794 of 2082)	38.3 % (535 of 1398)	38.1 % (249 of 654)	33.3 % (10 of 30)
Aromatic	33.6 % (153 of 456)	33.6 % (110 of 327)	33.3 % (42 of 126)	33.3 % (1 of 3)
Methyl	38.9 % (84 of 216)	38.3 % (46 of 120)	39.6 % (38 of 96)

1. vnd/NK-2 homeodomain

ASDGLPNKKR KRRVLFTKAQ TYELERRFRQ QRYLSAPERE HLASLIRLTP TQVKIWFQNH RYKTKRAQNE KGYEGHP

2. (+)5'TGTGTCAAGTGGCTGT

TGTGTCAAGT GGCTGT

3. (-)5'ACAGCCACTTGACACAA

ACAGCCACTT GACACAA

Show sample condition

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	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: 0.05 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: 0.05 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: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 1NK2, Strand ID: P Detail

Coupling constant

53 J values in 1 lists
Field strength (¹H) 600 MHz, Temperature 308 (±0.2) K, pH 6.0 (±0.2) Detail

Release date

2001-03-06

Citation 1

The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy
Gruschus, J.M., Tsao, D.H.H., Wang, L., Nirenberg, M., Ferretti, J.A.
J. Mol. Biol. (1999), 289, 529-545, PubMed 10356327 , DOI 10.1006/jmbi.1999.2774 , Abstract

Show more 3 citaions

Citation 2

Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity
Gruschus, J.M., Tsao, D.H., Wang, L.H., Nirenberg, M., Ferretti, J.A.
Biochemistry (1997), 36, 5372-5380, PubMed 9154919 , DOI 10.1021/bi9620060 , Abstract

Citation 3

The three-dimensional solution structure of the NK-2 homeodomain from Drosophila
Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., Ferretti, J.A.
J. Mol. Biol. (1995), 251, 297-307, PubMed 7643404 , DOI 10.1006/jmbi.1995.0435 , Abstract

Citation 4

Elongation of helix III of the NK-2 homeodomain upon binding to DNA: a secondary structure study by NMR
Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., Ferretti, J.A.
Biochemistry (1994), 33, 15053-15060, PubMed 7999763 , DOI 10.1021/bi00254a014 , Abstract

Hide non-primary 3 citaions

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P22808 released on 1991-08-01
Title VND_DROME Entity Homeobox protein vnd

Related entities 1. vnd/NK-2 homeodomain, : 1 : 2 : 3 : 134 entities Detail

Experiments performed 6 experiments Detail

1 1H-15N NOESY-HMQC

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

2 1H-13C NOESY-HSQC

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

3 1H-15N TOCSY

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

4 1H-15N HMQC-J

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

5 15N experiments in H2O

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

6 13C experiments in D2O

Instrument

Model Bruker AMX (600 MHz)

Sample #1

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
1	vnd/NK-2 homeodomain	[U13C; U-15N]	1.5 ~ 2.0 mM
2	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
3	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
4	NaCl		80 mM
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
7	vnd/NK-2 homeodomain	[U-15N]	1.5 ~ 2.0 mM
8	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
9	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
10	NaCl		80 mM
11	D2O		10 %
12	H2O		90 %

Sample #3

Temperature 308 (±0.2) K, pH 6.0 (±0.2)

#	Name	Isotope labeling	Concentration
13	vnd/NK-2 homeodomain	[U-13C; U-15N]	1.5 ~ 2.0 mM
14	(+)5'TGTGTCAAGTGGCTGT		1.425 ~ 1.9 mM
15	(-)5'ACAGCCACTTGACACAA		1.425 ~ 1.9 mM
16	NaCl		80 mM
17	D2O		100 %

nullKeywords dna-binding protein, embryonic development, homeodomain

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.92 seconds)

BMRB: 4141

Sample #1

Sample #2

Sample #3

Sample #1

Sample #2

Sample #3

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. vnd/NK-2 homeodomain, : 1 : 2 : 3 : 134 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3

Instrument

Sample #1

Sample #2

Sample #3