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BMRB: 17310

2HM9

L.casei DHFR-TRIMETHOPRIM complex

Authors

Polshakov, V.I., Birdsall, B., Feeney, J., Kovalevskaya, N.

Assembly

DHFR.TMP

Entity

1. DHFR (polymer, Thiol state: not present), 162 monomers, 18307.38 Da Detail

TAFLWAQDRD GLIGKDGHLP WHLPDDLHYF RAQTVGKIMV VGRRTYESFP KRPLPERTNV VLTHQEDYQA QGAVVVHDVA AVFAYAKQHP DQELVIAGGA QIFTAFKDDV DTLLVTRLAG SFEGDTKMIP LNWDDFTKVS SRTVEDTNPA LTHTYEVWQK KA

2. TRR (non-polymer), 291.326 Da

Total weight

18598.707 Da

Max. entity weight

18307.38 Da

Source organism

Lacticaseibacillus casei

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 76.8 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.8 % (1452 of 1890)	85.2 % (827 of 971)	61.9 % (464 of 749)	94.7 % (161 of 170)
Backbone	95.6 % (914 of 956)	97.2 % (317 of 326)	93.3 % (444 of 476)	99.4 % (153 of 154)
Sidechain	62.5 % (679 of 1086)	79.1 % (510 of 645)	37.9 % (161 of 425)	50.0 % (8 of 16)
Aromatic	43.4 % (85 of 196)	86.7 % (85 of 98)	0.0 % (0 of 94)	0.0 % (0 of 4)
Methyl	62.4 % (121 of 194)	99.0 % (96 of 97)	25.8 % (25 of 97)

1. DHFR

TAFLWAQDRD GLIGKDGHLP WHLPDDLHYF RAQTVGKIMV VGRRTYESFP KRPLPERTNV VLTHQEDYQA QGAVVVHDVA AVFAYAKQHP DQELVIAGGA QIFTAFKDDV DTLLVTRLAG SFEGDTKMIP LNWDDFTKVS SRTVEDTNPA LTHTYEVWQK KA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	DHFR	natural abundance	2 mM
8	Trimethoprim	natural abundance	2 mM
9	D2O	natural abundance	100 %
10	NaCl	natural abundance	100 mM
11	sodium phosphate buffer	natural abundance	50 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	DHFR	[U-98% 13C; U-98% 15N]	1 mM
13	Trimethoprim	natural abundance	1 mM
14	H2O	natural abundance	95 %
15	D2O	natural abundance	5 %
16	NaCl	natural abundance	100 mM
17	sodium phosphate buffer	natural abundance	50 mM

Release date

2012-01-03

Citation 1

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
Feeney, J., Birdsall, B., Kovalevskaya, N.V., Smurnyy, Y.D., Navarro Peran, E.M., Polshakov, V.I.
Biochemistry (2011), 50, 3609-3620, PubMed 21410224 , DOI 10.1021/bi200067t , Abstract

Show more 1 citaion

Citation 2

Structural Factors Determine the Selectivity of Antibacterial Drug Trimethoprim Binding to Dihydrofolate Reductase
Kovalevskaya, N.V., Smurnyy, Y.D., Birdsall, B., Feeney, J., Polshakov, V.I.
Pharm. Chem. J. (2007), 41, 350-353, PubMed , DOI:

Hide non-primary 1 citaion

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 17125 released on 2011-05-17
    Title SOLUTION STRUCTURE OF LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE APO-FORM, 25 CONFORMERS
  BMRB: 17311 released on 2011-03-29
    Title L.casei DHFR-NADPH complex

Related entities 1. DHFR, : 1 : 9 : 137 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

2 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	DHFR	natural abundance	2 mM
8	Trimethoprim	natural abundance	2 mM
9	D2O	natural abundance	100 %
10	NaCl	natural abundance	100 mM
11	sodium phosphate buffer	natural abundance	50 mM

3 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	DHFR	natural abundance	2 mM
8	Trimethoprim	natural abundance	2 mM
9	D2O	natural abundance	100 %
10	NaCl	natural abundance	100 mM
11	sodium phosphate buffer	natural abundance	50 mM

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	DHFR	natural abundance	2 mM
8	Trimethoprim	natural abundance	2 mM
9	D2O	natural abundance	100 %
10	NaCl	natural abundance	100 mM
11	sodium phosphate buffer	natural abundance	50 mM

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

6 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

7 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

8 3D HNHB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

9 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	DHFR	[U-98% 13C; U-98% 15N]	1 mM
13	Trimethoprim	natural abundance	1 mM
14	H2O	natural abundance	95 %
15	D2O	natural abundance	5 %
16	NaCl	natural abundance	100 mM
17	sodium phosphate buffer	natural abundance	50 mM

10 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	DHFR	[U-98% 13C; U-98% 15N]	1 mM
13	Trimethoprim	natural abundance	1 mM
14	H2O	natural abundance	95 %
15	D2O	natural abundance	5 %
16	NaCl	natural abundance	100 mM
17	sodium phosphate buffer	natural abundance	50 mM

11 2D 1H-15N IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

12 2D 1H-15N IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	DHFR	[U-98% 15N]	1.0 ~ 3.0 mM
2	Trimethoprim	natural abundance	1.0 ~ 3.0 mM
3	H2O	natural abundance	95 %
4	D2O	natural abundance	5 %
5	NaCl	natural abundance	100 mM
6	sodium phosphate buffer	natural abundance	50 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr17310_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
2	1	TRR	2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM	Assigned chemical shifts

Content subtype: bmr17310_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_protein	Warning	1623		100.0 (chain: 1, length: 162), 100.0 (chain: 2, length: 1)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_protein
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 162, Sequence coverage: 100.0%
  - Entity_assembly_ID: 2, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 1022
  - ¹³C chemical shifts: 440
  - ¹⁵N chemical shifts: 161
- Completeness of assignments
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 2
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	971	807	83.1
¹³C chemical shifts	749	440	58.7
¹⁵N chemical shifts	178	161	90.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	326	314	96.3
¹³C chemical shifts	324	300	92.6
¹⁵N chemical shifts	154	153	99.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	645	493	76.4
¹³C chemical shifts	425	140	32.9
¹⁵N chemical shifts	24	8	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	98	99.0
¹³C chemical shifts	99	14	14.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	85	86.7
¹³C chemical shifts	94	0	0.0
¹⁵N chemical shifts	4	0	0.0

Comp_index_ID	Comp_ID
1	TRR

Keywords cooperative binding, DHFR, protein-ligand interactions, protein structure, tromethoprim

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Found 1 Document (0.531 seconds)

BMRB: 17310

Sample #1

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Sample #3

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. DHFR, : 1 : 9 : 137 entities Detail

Experiments performed 12 experiments Detail

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Chemical shift validation 4 contents Detail