BMRB Entry 4141

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PDB ID: 1nk2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR4141
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

1998-05-11

Original release date:

2001-03-07

Authors:

Gruschus, James; Tsao, Desiree; Wang, Lan-Hsiang; Nirenberg, Marshall; Ferretti, James

Citation:

Citation: Gruschus, James; Tsao, Desiree; Wang, Lan-Hsiang; Nirenberg, Marshall; Ferretti, James. "The three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex by NMR spectroscopy" J. Mol. Biol. 289, 529-545 (1999).
PubMed: 10356327

Assembly members:

Assembly members:
vnd/NK-2 homeodomain, polymer, 77 residues, Formula weight is not available
(+)5'TGTGTCAAGTGGCTGT, polymer, 16 residues, Formula weight is not available
(-)5'ACAGCCACTTGACACAA, polymer, 16 residues, Formula weight is not available

Natural source:

Natural source: Common Name: fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
vnd/NK-2 homeodomain: ASDGLPNKKRKRRVLFTKAQ TYELERRFRQQRYLSAPERE HLASLIRLTPTQVKIWFQNH RYKTKRAQNEKGYEGHP
(+)5'TGTGTCAAGTGGCTGT: TGTGTCAAGTGGCTGT
(-)5'ACAGCCACTTGACACAA: ACAGCCACTTGACACAA

Data sets:

assigned_chemical_shifts
coupling_constants
- coupling_constant

Data type	Count
13C chemical shifts	291
15N chemical shifts	100
1H chemical shifts	904
31P chemical shifts	18
coupling constants	53

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	vnd/NK-2 homeodomain	1
2	DNA duplex (+) strand	2
3	DNA duplex (-) strand	3

Entities:

Entity 1, vnd/NK-2 homeodomain 77 residues - Formula weight is not available

1

ALA

SER

ASP

GLY

LEU

PRO

ASN

LYS

ARG

2

LYS

ARG

VAL

LEU

PHE

THR

LYS

ALA

GLN

3

THR

TYR

GLU

LEU

GLU

ARG

PHE

ARG

GLN

4

GLN

ARG

TYR

LEU

SER

ALA

PRO

GLU

ARG

GLU

5

HIS

LEU

ALA

SER

LEU

ILE

ARG

LEU

THR

PRO

6

THR

GLN

VAL

LYS

ILE

TRP

PHE

GLN

ASN

HIS

7

ARG

TYR

LYS

THR

LYS

ARG

ALA

GLN

ASN

GLU

8

LYS

GLY

TYR

GLU

GLY

HIS

PRO

Entity 2, DNA duplex (+) strand 16 residues - Formula weight is not available

1

DT

DG

DT

DG

DT

DC

DA

DG

DT

2

DG

DC

DT

DG

DT

Entity 3, DNA duplex (-) strand 16 residues - Formula weight is not available

1

DA

DC

DA

DG

DC

DA

DC

DT

2

DG

DA

DC

DA

DC

DA

Samples:

sample_1: vnd/NK-2 homeodomain, [U13C; U-15N], 1.5 – 2.0 mM; (+)5'TGTGTCAAGTGGCTGT1.425 – 1.9 mM; (-)5'ACAGCCACTTGACACAA1.425 – 1.9 mM; NaCl 80 mM; D2O 10%; H2O 90%

sample_2: vnd/NK-2 homeodomain, [U-15N], 1.5 – 2.0 mM; (+)5'TGTGTCAAGTGGCTGT1.425 – 1.9 mM; (-)5'ACAGCCACTTGACACAA1.425 – 1.9 mM; NaCl 80 mM; D2O 10%; H2O 90%

sample_3: vnd/NK-2 homeodomain, [U-13C; U-15N], 1.5 – 2.0 mM; (+)5'TGTGTCAAGTGGCTGT1.425 – 1.9 mM; (-)5'ACAGCCACTTGACACAA1.425 – 1.9 mM; NaCl 80 mM; D2O 100%

cond_1: ionic strength: 0.08 M; pH: 6.0; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-15N NOESY-HMQC	not available	not available	cond_1
1H-13C NOESY-HSQC	not available	not available	cond_1
1H-15N TOCSY	not available	not available	cond_1
1H-15N HMQC-J	not available	not available	cond_1
15N experiments in H2O	not available	not available	cond_1
13C experiments in D2O	not available	not available	cond_1

Software:

NMRPipe - Fourier transformation

NMR spectrometers:

Bruker AMX 600 MHz

BMRB	4368
PDB	1NK2 1NK3 1QRY 1VND
EMBL	CAA21410 CAA60619
GB	AAA28617 AAB34960 AAF45521 ABI30961 ADJ13174
REF	NP_001036253 NP_476786 XP_001354499 XP_001982405 XP_001992446
SP	P22808
AlphaFold	P22808