BMRB Entry 16441

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16441
MolProbity Validation Chart

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Title:
Solution structure of the nucleotide binding domain of the human Menkes protein in the ATP-bound form
Deposition date:
2009-08-05
Original release date:
2009-11-19
Authors:
Banci, Lucia; Bertini, Ivano; Cantini, Francesca; Inagaki, Sayaka; Migliardi, Manuele; Rosato, Antonio
Citation:

Citation: Banci, Lucia; Bertini, Ivano; Cantini, Francesca; Inagaki, Sayaka; Migliardi, Manuele; Rosato, Antonio. "The Binding Mode of ATP Revealed by the Solution Structure of the N-domain of Human ATP7A."  J. Biol. Chem. 285, 2537-2544 (2010).
PubMed: 19917612

Assembly members:

Assembly members:
N-MNK, polymer, 185 residues, 19803.387 Da.
ATP, non-polymer, 507.181 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pETG-30A

Entity Sequences (FASTA):

Entity Sequences (FASTA):
N-MNK: SFTMHGTPVVNQVKVLTESN RISHHKILAIVGTAESNSEH PLGTAITKYCKQELDTETLG TCIDFQVVPGCGISCKVTNI EGLLHKNNWNIEDNNIKNAS LVQIDASNEQSSTSSSMIID AQISNALNAQQYKVLIGNRE WMIRNGLVINNDVNDFMTEH ERKGRTAVLVAVDDELCGLI AIADT

Data sets:
Data typeCount
13C chemical shifts675
15N chemical shifts193
1H chemical shifts1186

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1N-MNK1
2ATP2

Entities:

Entity 1, N-MNK 185 residues - 19803.387 Da.

After cleavage of the tag, four amino acids (SFTM) from the restriction site are left at the N-terminus of the protein.

1   SERPHETHRMETHISGLYTHRPROVALVAL
2   ASNGLNVALLYSVALLEUTHRGLUSERASN
3   ARGILESERHISHISLYSILELEUALAILE
4   VALGLYTHRALAGLUSERASNSERGLUHIS
5   PROLEUGLYTHRALAILETHRLYSTYRCYS
6   LYSGLNGLULEUASPTHRGLUTHRLEUGLY
7   THRCYSILEASPPHEGLNVALVALPROGLY
8   CYSGLYILESERCYSLYSVALTHRASNILE
9   GLUGLYLEULEUHISLYSASNASNTRPASN
10   ILEGLUASPASNASNILELYSASNALASER
11   LEUVALGLNILEASPALASERASNGLUGLN
12   SERSERTHRSERSERSERMETILEILEASP
13   ALAGLNILESERASNALALEUASNALAGLN
14   GLNTYRLYSVALLEUILEGLYASNARGGLU
15   TRPMETILEARGASNGLYLEUVALILEASN
16   ASNASPVALASNASPPHEMETTHRGLUHIS
17   GLUARGLYSGLYARGTHRALAVALLEUVAL
18   ALAVALASPASPGLULEUCYSGLYLEUILE
19   ALAILEALAASPTHR

Entity 2, ATP - C10 H16 N5 O13 P3 - 507.181 Da.

1   ATP

Samples:

sample_1: N-MNK, [U-99% 15N], 1.2 – 1.5 mM; ATP1.2 – 1.5 mM; phosphate 50 mM; DTT 2 mM; D2O 10%; H2O 90%

sample_2: N-MNK, [U-95% 13C; U-95% 15N], 0.8 – 1.0 mM; ATP0.8 – 1.0 mM; phosphate 50 mM; DTT 2 mM; D2O 10%; H2O 90%

sample_conditions_1: ionic strength: 0.05 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

CARA, Keller and Wuthrich - chemical shift assignment

XEASY, Bartels et al. - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

PSVS, Bhattacharya and Montelione - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PIR S36149
SWS NP_000043.3
BMRB 16440
PDB
DBJ BAG61422
EMBL CAB08162 CAB94714
GB AAA35580 AAA96010 AAI56438 EAW98605 EAW98606
REF NP_000043 NP_001269153 XP_002831882 XP_003824455 XP_004064479
SP Q04656
AlphaFold Q04656

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks