BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 17310

Title: L.casei DHFR-TRIMETHOPRIM complex   PubMed: 21410224

Authors: Polshakov, Vladimir; Birdsall, Berry; Feeney, James; Kovalevskaya, Nadezhda

Citation: Feeney, James; Birdsall, Berry; Kovalevskaya, Nadezhda; Smurnyy, Yegor; Navarro Peran, Emna; Polshakov, Vladimir. "NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions."  Biochemistry 50, 3609-3620 (2011).

Assembly members:
DHFR, polymer, 162 residues, Formula weight is not available
TRR, non-polymer, 291.326 Da.

Natural source:   Common Name: Lactobacillus casei   Taxonomy ID: 1582   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Lactobacillus casei

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

Entity Sequences (FASTA):
DHFR: TAFLWAQDRDGLIGKDGHLP WHLPDDLHYFRAQTVGKIMV VGRRTYESFPKRPLPERTNV VLTHQEDYQAQGAVVVHDVA AVFAYAKQHPDQELVIAGGA QIFTAFKDDVDTLLVTRLAG SFEGDTKMIPLNWDDFTKVS SRTVEDTNPALTHTYEVWQK KA

Data sets:
Data typeCount
13C chemical shifts440
15N chemical shifts161
1H chemical shifts1022

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DHFR1
2TRR2

Entities:

Entity 1, DHFR 162 residues - Formula weight is not available

1   THRALAPHELEUTRPALAGLNASPARGASP
2   GLYLEUILEGLYLYSASPGLYHISLEUPRO
3   TRPHISLEUPROASPASPLEUHISTYRPHE
4   ARGALAGLNTHRVALGLYLYSILEMETVAL
5   VALGLYARGARGTHRTYRGLUSERPHEPRO
6   LYSARGPROLEUPROGLUARGTHRASNVAL
7   VALLEUTHRHISGLNGLUASPTYRGLNALA
8   GLNGLYALAVALVALVALHISASPVALALA
9   ALAVALPHEALATYRALALYSGLNHISPRO
10   ASPGLNGLULEUVALILEALAGLYGLYALA
11   GLNILEPHETHRALAPHELYSASPASPVAL
12   ASPTHRLEULEUVALTHRARGLEUALAGLY
13   SERPHEGLUGLYASPTHRLYSMETILEPRO
14   LEUASNTRPASPASPPHETHRLYSVALSER
15   SERARGTHRVALGLUASPTHRASNPROALA
16   LEUTHRHISTHRTYRGLUVALTRPGLNLYS
17   LYSALA

Entity 2, TRR - C14 H19 N4 O3 - 291.326 Da.

1   TRR

Samples:

sample_1: DHFR, [U-98% 15N], 1 – 3 mM; Trimethoprim1 – 3 mM; H2O 95%; D2O 5%; NaCl 100 mM; sodium phosphate buffer 50 mM

sample_2: DHFR 2 mM; Trimethoprim 2 mM; D2O 100%; NaCl 100 mM; sodium phosphate buffer 50 mM

sample_3: DHFR, [U-98% 13C; U-98% 15N], 1 mM; Trimethoprim 1 mM; H2O 95%; D2O 5%; NaCl 100 mM; sodium phosphate buffer 50 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
2D 1H-15N IPAPsample_1isotropicsample_conditions_1
2D 1H-15N IPAPsample_1anisotropicsample_conditions_1

Software:

VNMR, Varian - collection

xwinnmr, Bruker Biospin - collection

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

SPARKY, Goddard - data analysis

AngleSearch, Polshakov VI & Feeney J. - data analysis

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 600 MHz
  • Varian INOVA 800 MHz

Related Database Links:

BMRB 17125 17311 3524 3525 4262
PDB
DBJ BAI41869
EMBL CAR87293 CAR90253 CDN23977
GB AAA25237 AER64174 AGP71178 AGP74091 EDY98474
PRF 0309272A 1107232A
REF WP_005686414 WP_005689288 WP_014569635 WP_033573062 WP_047676754
SP P00381