BMRB Entry 17125

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17125
MolProbity Validation Chart

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Title:
SOLUTION STRUCTURE OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE APO-FORM, 25 CONFORMERS
Deposition date:
2010-08-12
Original release date:
2011-05-18
Authors:
Polshakov, Vladimir; Birdsall, Berry; Feeney, James
Citation:

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).
PubMed: 21410224

Assembly members:

Assembly members:
DHFR, polymer, 162 residues, 18331.770 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PMT702

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
13C chemical shifts564
15N chemical shifts152
1H chemical shifts1032
H exchange protection factors54

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1apo DHFR1

Entities:

Entity 1, apo DHFR 162 residues - 18331.770 Da.

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

Samples:

sample_1: DHFR 2 mM; potassium chloride 100 mM; potassium phosphate 50 mM; sodium azide 0.1%; D2O 100%

sample_2: DHFR, [U-99% 13C; U-99% 15N], 1 mM; potassium chloride 100 mM; potassium phosphate 50 mM; sodium azide 0.1%; D2O 10%; H2O 90%

sample_3: DHFR, [U-99% 15N], 1 mM; potassium chloride 100 mM; potassium phosphate 50 mM; sodium azide 0.1%; D2O 5%; H2O 95%

sample_4: DHFR, [U-99% 15N], 1 mM; potassium chloride 100 mM; potassium phosphate 50 mM; sodium azide 0.1%; DMPC/DHPC 5%; D2O 5%; H2O 95%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HNHAsample_3isotropicsample_conditions_1
3D HNHBsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 15N-rejected NOESYsample_3isotropicsample_conditions_1
2D IPAPsample_4anisotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

VNMR v6.1, Varian - collection

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

AngleSearch, Polshakov VI & Feeney J. - geometry optimization

NMRest, Polshakov VI - data analysis

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

ProcheckNMR, Laskowski and MacArthur - data analysis

InsightII v2000, Accelrys Software Inc. - data analysis

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz
  • Bruker Avance 600 MHz
  • Varian UnityPlus 500 MHz

Related Database Links:

BMRB 17310 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
AlphaFold P00381

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