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Biological Magnetic Resonance Data Bank


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BMRB Entry 17311

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR17311
MolProbity Validation Chart

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

Deposition date: 2010-11-22 Original release date: 2011-03-30

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
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, non-polymer, 745.421 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 shifts592
15N chemical shifts173
1H chemical shifts1131

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DHFR1
2NADPH2

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, NADPH - C21 H30 N7 O17 P3 - 745.421 Da.

1   NDP

Samples:

sample_1: DHFR, [U-98% 15N], 1 – 3 mM; NADPH1 – 3 mM; H2O 95%; D2O 5%

sample_2: DHFR 2 mM; NADPH 2 mM; D2O 100%

sample_3: DHFR, [U-98% 13C; U-98% 15N], 1 mM; NADPH 1 mM; H2O 95%; D2O 5%

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
3D HNHAsample_1isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HCCH-COSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
2D 1H-15N IPAPsample_1isotropicsample_conditions_1
2D 1H-15N IPAPsample_1anisotropicsample_conditions_1
2D 15N-rejected NOESYsample_1isotropicsample_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
  • Bruker Avance 700 MHz
  • Varian INOVA 800 MHz

Related Database Links:

BMRB 17125 17310 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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts