BMRB Entry 50749

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50749

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Ligand-induced structural transition combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in crowded spectra
Deposition date:
2021-02-08
Original release date:
2022-04-15
Authors:
Muehlberg, Lars; Alarcin, Tuncay; Maass, Thorben; Kuechler, Richard; Mallagaray, Alvaro
Citation:
Assembly members:

Assembly members:
entity_1, polymer, 505 residues, Formula weight is not available
entity_UTP, non-polymer, 484.141 Da.
entity_MG, non-polymer, 24.305 Da.

Natural source:

Natural source:   Common Name: Leishmania major   Taxonomy ID: 5664   Superkingdom: Eukaryota   Kingdom: not available   Genus/species: Leishmania major

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MENDMKSLSAAAQACVKKMR DAKVNEACIRTFIAQHVMVS KGETGSIPDSAIMPVDSLDA LDSLTIECDNAVLQSTVVLK LNGGLGTGMGLCDAKTLLEV KDGKTFLDFTALQVQYLRQH CSEHLRFMLMDSFNTSASTK SFLKARYPWLYQVFDSEVEL MQNQVPKILQDTLEPAAWAE NPAYEWAPPGHGDIYTALYG SGKLQELVEQGYRYMFVSNG DNLGATIDKRVLAYMEKEKI DFLMEVCRRTESDKKGGHLA RQTVYVKGKDGQPDAEKRVL LLRESAQCPKADMESFQDIN KYSFFNTNNLWIRLPVLLET MQEHGGTLPLPVIRNEKTVD SSNSASPKVYQLETAMGAAI AMFESASAIVVPRSRFAPVK TCADLLALRSDAYVVTDDFR LVLDDRCHGHPPVVDLDSAH YKMMNGFEKLVQHGVPSLVE CKRVTVKGLVQFGAGNVLTG TVTIENTDSASAFVIPDGAK LNDTTASPQQSTNKMRPLEH HHHHH

Data sets:
Data typeCount
13C chemical shifts199
1H chemical shifts597

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1LmUGP1
2UTP2
3MG3

Entities:

Entity 1, LmUGP 505 residues - Formula weight is not available

1   METGLUASNASPMETLYSSERLEUSERALA
2   ALAALAGLNALACYSVALLYSLYSMETARG
3   ASPALALYSVALASNGLUALACYSILEARG
4   THRPHEILEALAGLNHISVALMETVALSER
5   LYSGLYGLUTHRGLYSERILEPROASPSER
6   ALAILEMETPROVALASPSERLEUASPALA
7   LEUASPSERLEUTHRILEGLUCYSASPASN
8   ALAVALLEUGLNSERTHRVALVALLEULYS
9   LEUASNGLYGLYLEUGLYTHRGLYMETGLY
10   LEUCYSASPALALYSTHRLEULEUGLUVAL
11   LYSASPGLYLYSTHRPHELEUASPPHETHR
12   ALALEUGLNVALGLNTYRLEUARGGLNHIS
13   CYSSERGLUHISLEUARGPHEMETLEUMET
14   ASPSERPHEASNTHRSERALASERTHRLYS
15   SERPHELEULYSALAARGTYRPROTRPLEU
16   TYRGLNVALPHEASPSERGLUVALGLULEU
17   METGLNASNGLNVALPROLYSILELEUGLN
18   ASPTHRLEUGLUPROALAALATRPALAGLU
19   ASNPROALATYRGLUTRPALAPROPROGLY
20   HISGLYASPILETYRTHRALALEUTYRGLY
21   SERGLYLYSLEUGLNGLULEUVALGLUGLN
22   GLYTYRARGTYRMETPHEVALSERASNGLY
23   ASPASNLEUGLYALATHRILEASPLYSARG
24   VALLEUALATYRMETGLULYSGLULYSILE
25   ASPPHELEUMETGLUVALCYSARGARGTHR
26   GLUSERASPLYSLYSGLYGLYHISLEUALA
27   ARGGLNTHRVALTYRVALLYSGLYLYSASP
28   GLYGLNPROASPALAGLULYSARGVALLEU
29   LEULEUARGGLUSERALAGLNCYSPROLYS
30   ALAASPMETGLUSERPHEGLNASPILEASN
31   LYSTYRSERPHEPHEASNTHRASNASNLEU
32   TRPILEARGLEUPROVALLEULEUGLUTHR
33   METGLNGLUHISGLYGLYTHRLEUPROLEU
34   PROVALILEARGASNGLULYSTHRVALASP
35   SERSERASNSERALASERPROLYSVALTYR
36   GLNLEUGLUTHRALAMETGLYALAALAILE
37   ALAMETPHEGLUSERALASERALAILEVAL
38   VALPROARGSERARGPHEALAPROVALLYS
39   THRCYSALAASPLEULEUALALEUARGSER
40   ASPALATYRVALVALTHRASPASPPHEARG
41   LEUVALLEUASPASPARGCYSHISGLYHIS
42   PROPROVALVALASPLEUASPSERALAHIS
43   TYRLYSMETMETASNGLYPHEGLULYSLEU
44   VALGLNHISGLYVALPROSERLEUVALGLU
45   CYSLYSARGVALTHRVALLYSGLYLEUVAL
46   GLNPHEGLYALAGLYASNVALLEUTHRGLY
47   THRVALTHRILEGLUASNTHRASPSERALA
48   SERALAPHEVALILEPROASPGLYALALYS
49   LEUASNASPTHRTHRALASERPROGLNGLN
50   SERTHRASNLYSMETARGPROLEUGLUHIS
51   HISHISHISHISHIS

Entity 2, UTP - C9 H15 N2 O15 P3 - 484.141 Da.

1   UTP

Entity 3, MG - Mg - 24.305 Da.

1   MG

Samples:

sample_1: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 450 uM; Magnesium 5000 uM

sample_2: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 450 uM; Magnesium 5000 uM; Uridine-5'-diphosphate-glucose (UDP-glucose) 12000 uM

sample_3: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met 1H,13C-methyl labeled, 267 uM; Magnesium 5000 uM

sample_4: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Ala 1H,13C-methyl labeled, 250 uM; Magnesium 5000 uM

sample_5: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Ile 1H,13C-methyl labeled, 200 uM; Magnesium 5000 uM

sample_6: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Leu (proS) and Val (proS) 1H,13C-methyl labeled, 312 uM; Magnesium 5000 uM

sample_7: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Val (proS) 1H,13C-methyl labeled, 250 uM; Magnesium 5000 uM

sample_8: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 100 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Lanthanum 0 - 2100 uM

sample_9: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 100 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Lutetium 0 - 2100 uM

sample_10: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 10 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Terbium 0 - 2100 uM

sample_11: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 100 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Thulium 0 - 2100 uM

sample_12: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 100 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Europium 0 - 2100 uM

sample_13: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 100 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Europium 0 - 2100 uM

sample_14: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 199 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Magnesium 50 uM

sample_15: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 199 uM; Uridine-5'-triphosphate (UTP) 3500 uM; Manganese 50 uM

sample_16: UDP-Glucose pyrophosphorylase from Leishmania major (LmUGP), [U-2H], Met, Ile, Leu (proS), Val (proS), Ala and Thr 1H,13C-methyl labeled, 110 - 145 uM; Uridine-5'-triphosphate (UTP) 0 - 10000 uM; Uridine-5'-diphosphate-glucose (UDP-glucose) 0 - 10000 uM; Magnesium 10000 uM

sample_conditions_1: pH*: 7.13; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
4D CC NOESYsample_1isotropicsample_conditions_1
4D CC NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HMQCsample_3isotropicsample_conditions_1
2D 1H-13C HMQCsample_4isotropicsample_conditions_1
2D 1H-13C HMQCsample_5isotropicsample_conditions_1
2D 1H-13C HMQCsample_6isotropicsample_conditions_1
2D 1H-13C HMQCsample_7isotropicsample_conditions_1
2D 1H-13C HMQCsample_8isotropicsample_conditions_1
2D 1H-13C HMQCsample_9isotropicsample_conditions_1
2D 1H-13C HMQCsample_10anisotropicsample_conditions_1
2D 1H-13C HMQCsample_11anisotropicsample_conditions_1
2D 1H-13C HMQCsample_12anisotropicsample_conditions_1
2D 1H-13C HMQCsample_13anisotropicsample_conditions_1
T2/R2 relaxationsample_14isotropicsample_conditions_1
T2/R2 relaxationsample_15anisotropicsample_conditions_1
2D 1H-13C HMQCsample_16isotropicsample_conditions_1

Software:

CcpNMR vv2.4.2 - chemical shift assignment, chemical shift calculation, peak picking

TOPSPIN v4.0.2 - collection, processing

MAP-XSII vv2 - automated chemical shift assignment

CH3Shift vv2 - Prediction of methyl chemical shifts of Ala, Ile, Leu (proS), Val (proS) and Thr

ShiftX2 vv1.10 - Prediction of chemical shifts of methionines

MoodLoop vmain.74d15d3 - Modeling of N- and C-termini

MATLAB vR2020b - data analysis

Paramagpy - Calculation of Chi-tensors and metal position based on pseudocontact shifts and available structural models

NMR spectrometers:

  • Bruker AVANCE III 950 MHz
  • Bruker AVANCE III 900 MHz
  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 500 MHz