BMRB Entry 11506

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11506
MolProbity Validation Chart

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Title:
Solution structure of human full-length vaccinia related kinase 1 (VRK1)
Deposition date:
2012-07-12
Original release date:
2013-12-02
Authors:
Koshiba, Seizo; Tochio, Naoya; Yokoyama, Jun; Kigawa, Takanori
Citation:

Citation: Koshiba, Seizo; Tochio, Naoya; Yokoyama, Jun; Yoon, Ho Sup; Kigawa, Takanori. "A strategy for structure determination of large molecular weight protein using isotope labeling methodology with cell-free protein systhesis: application to 45 kDa human vaccinia related kianse 1 (VRK1)"  .

Assembly members:

Assembly members:
entity, polymer, 403 residues, 46071.996 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: E. coli - cell free   Vector: P060908-04

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSSGSSGMPRVKAAQAGRQS SAKRHLAEQFAVGEIITDMA KKEWKVGLPIGQGGFGCIYL ADMNSSESVGSDAPCVVKVE PSDNGPLFTELKFYQRAAKP EQIQKWIRTRKLKYLGVPKY WGSGLHDKNGKSYRFMIMDR FGSDLQKIYEANAKRFSRKT VLQLSLRILDILEYIHEHEY VHGDIKASNLLLNYKNPDQV YLVDYGLAYRYCPEGVHKEY KEDPKRCHDGTIEFTSIDAH NGVAPSRRGDLEILGYCMIQ WLTGHLPWEDNLKDPKYVRD SKIRYRENIASLMDKCFPEK NKPGEIAKYMETVKLLDYTE KPLYENLRDILLQGLKAIGS KDDGKLDLSVVENGGLKAKT ITKKRKKEIEESKEPGVEDT EWSNTQTEEAIQTRSRTRKR VQK

Data sets:
Data typeCount
13C chemical shifts1305
15N chemical shifts349
1H chemical shifts947

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 403 residues - 46071.996 Da.

1   GLYSERSERGLYSERSERGLYMETPROARG
2   VALLYSALAALAGLNALAGLYARGGLNSER
3   SERALALYSARGHISLEUALAGLUGLNPHE
4   ALAVALGLYGLUILEILETHRASPMETALA
5   LYSLYSGLUTRPLYSVALGLYLEUPROILE
6   GLYGLNGLYGLYPHEGLYCYSILETYRLEU
7   ALAASPMETASNSERSERGLUSERVALGLY
8   SERASPALAPROCYSVALVALLYSVALGLU
9   PROSERASPASNGLYPROLEUPHETHRGLU
10   LEULYSPHETYRGLNARGALAALALYSPRO
11   GLUGLNILEGLNLYSTRPILEARGTHRARG
12   LYSLEULYSTYRLEUGLYVALPROLYSTYR
13   TRPGLYSERGLYLEUHISASPLYSASNGLY
14   LYSSERTYRARGPHEMETILEMETASPARG
15   PHEGLYSERASPLEUGLNLYSILETYRGLU
16   ALAASNALALYSARGPHESERARGLYSTHR
17   VALLEUGLNLEUSERLEUARGILELEUASP
18   ILELEUGLUTYRILEHISGLUHISGLUTYR
19   VALHISGLYASPILELYSALASERASNLEU
20   LEULEUASNTYRLYSASNPROASPGLNVAL
21   TYRLEUVALASPTYRGLYLEUALATYRARG
22   TYRCYSPROGLUGLYVALHISLYSGLUTYR
23   LYSGLUASPPROLYSARGCYSHISASPGLY
24   THRILEGLUPHETHRSERILEASPALAHIS
25   ASNGLYVALALAPROSERARGARGGLYASP
26   LEUGLUILELEUGLYTYRCYSMETILEGLN
27   TRPLEUTHRGLYHISLEUPROTRPGLUASP
28   ASNLEULYSASPPROLYSTYRVALARGASP
29   SERLYSILEARGTYRARGGLUASNILEALA
30   SERLEUMETASPLYSCYSPHEPROGLULYS
31   ASNLYSPROGLYGLUILEALALYSTYRMET
32   GLUTHRVALLYSLEULEUASPTYRTHRGLU
33   LYSPROLEUTYRGLUASNLEUARGASPILE
34   LEULEUGLNGLYLEULYSALAILEGLYSER
35   LYSASPASPGLYLYSLEUASPLEUSERVAL
36   VALGLUASNGLYGLYLEULYSALALYSTHR
37   ILETHRLYSLYSARGLYSLYSGLUILEGLU
38   GLUSERLYSGLUPROGLYVALGLUASPTHR
39   GLUTRPSERASNTHRGLNTHRGLUGLUALA
40   ILEGLNTHRARGSERARGTHRARGLYSARG
41   VALGLNLYS

Samples:

sample_1: entity, [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL, ALA METHYL; 1H MET METHYL,GAMMA; 1H PHE EPSILON] VRK1, 0.4 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; glutamic acid 50 mM; arginine 50 mM; DTT, [U-2H], 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: entity, [U-13C; U-15N; U-2H; 1H ILE, LEU, VAL METHYL; 1H PHE, TYR EPSILON] VRK1, 0.4 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; glutamic acid 50 mM; arginine 50 mM; DTT, [U-2H], 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_3: entity, [U-15N; U-2H; 13C,1H ILE, LEU, VAL METHYL; 13C,1H PHE DELTA/EPSILON/ZETA] VRK1, 0.4 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; glutamic acid 50 mM; arginine 50 mM; DTT, [U-2H], 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_4: entity, SAIL-VRK1, 0.4 mM; TRIS, [U-2H], 20 mM; sodium chloride 100 mM; glutamic acid 50 mM; arginine 50 mM; DTT, [U-2H], 1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 13C-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 13C-13C NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

AZARA, Boucher - processing

NMRView, Johnson, One Moon Scientific - data analysis

Kujira, N. Kobayashi - data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • Bruker Avance 900 MHz

Related Database Links:

BMRB 16715 16738
PDB
DBJ BAA19108 BAF82799 BAI47070
GB AAI03762 AAI12076 AAI13511 AAQ02593 AIC55301
REF NP_001244605 NP_003375 XP_003902302 XP_004055717 XP_005562233
SP Q99986
AlphaFold Q99986

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