BMRB Entry 51004

Name: Role of active site loop dynamics in ligand release from E. coli dihydrofolate reductase
Published: 2021-07-09

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51004

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Role of active site loop dynamics in ligand release from E. coli dihydrofolate reductase

Deposition date:

2021-07-01

Original release date:

2021-07-09

Authors:

Singh, Amrinder; Fenwick, Robert; Dyson, Helen; Wright, Peter

Citation:

Citation: Singh, Amrinder; Fenwick, Robert; Dyson, Helen; Wright, Peter. "Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase" Biochemistry 60, 2663-2671 (2021).
PubMed: 34428034

Assembly members:

Assembly members:
entity_1, polymer, 160 residues, Formula weight is not available
entity_DDF, non-polymer, 443.453 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MISLIAALAVDRVIGMENAM PWPPLPADLAWFKRNTLNKP VIMGRHTWESIGRPLPGRKN IILSSQPGTDDRVTWVKSVD EAIAACGDVPEIMVIGGGRV YEQFLPKAQKLYLTHIDAEV EGDTHFPDYEPDDWESVFSE FHDADAQNAHSYCFEILERR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	129
1H chemical shifts	129

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	N23PPS148A E.coli DHFR	1
2	ddTHF	2

Entities:

Entity 1, N23PPS148A E.coli DHFR 160 residues - Formula weight is not available

1	MET	ILE	SER	LEU	ILE	ALA	ALA	LEU	ALA	VAL
2	ASP	ARG	VAL	ILE	GLY	MET	GLU	ASN	ALA	MET
3	PRO	TRP	PRO	PRO	LEU	PRO	ALA	ASP	LEU	ALA
4	TRP	PHE	LYS	ARG	ASN	THR	LEU	ASN	LYS	PRO
5	VAL	ILE	MET	GLY	ARG	HIS	THR	TRP	GLU	SER
6	ILE	GLY	ARG	PRO	LEU	PRO	GLY	ARG	LYS	ASN
7	ILE	ILE	LEU	SER	SER	GLN	PRO	GLY	THR	ASP
8	ASP	ARG	VAL	THR	TRP	VAL	LYS	SER	VAL	ASP
9	GLU	ALA	ILE	ALA	ALA	CYS	GLY	ASP	VAL	PRO
10	GLU	ILE	MET	VAL	ILE	GLY	GLY	GLY	ARG	VAL
11	TYR	GLU	GLN	PHE	LEU	PRO	LYS	ALA	GLN	LYS
12	LEU	TYR	LEU	THR	HIS	ILE	ASP	ALA	GLU	VAL
13	GLU	GLY	ASP	THR	HIS	PHE	PRO	ASP	TYR	GLU
14	PRO	ASP	ASP	TRP	GLU	SER	VAL	PHE	SER	GLU
15	PHE	HIS	ASP	ALA	ASP	ALA	GLN	ASN	ALA	HIS
16	SER	TYR	CYS	PHE	GLU	ILE	LEU	GLU	ARG	ARG

Entity 2, ddTHF - C21 H25 N5 O6 - 443.453 Da.

1

DDF

Samples:

sample_1: N23PPS148A E.coli DHFR, [U-100% 13C; U-100% 15N], 450 uM

sample_conditions_1: ionic strength: 0.075 M; pH: 7.6; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCACONH	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 800 MHz

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

1	MET	ILE	SER	LEU	ILE	ALA	ALA	LEU	ALA	VAL
2	ASP	ARG	VAL	ILE	GLY	MET	GLU	ASN	ALA	MET
3	PRO	TRP	PRO	PRO	LEU	PRO	ALA	ASP	LEU	ALA
4	TRP	PHE	LYS	ARG	ASN	THR	LEU	ASN	LYS	PRO
5	VAL	ILE	MET	GLY	ARG	HIS	THR	TRP	GLU	SER
6	ILE	GLY	ARG	PRO	LEU	PRO	GLY	ARG	LYS	ASN
7	ILE	ILE	LEU	SER	SER	GLN	PRO	GLY	THR	ASP
8	ASP	ARG	VAL	THR	TRP	VAL	LYS	SER	VAL	ASP
9	GLU	ALA	ILE	ALA	ALA	CYS	GLY	ASP	VAL	PRO
10	GLU	ILE	MET	VAL	ILE	GLY	GLY	GLY	ARG	VAL
11	TYR	GLU	GLN	PHE	LEU	PRO	LYS	ALA	GLN	LYS
12	LEU	TYR	LEU	THR	HIS	ILE	ASP	ALA	GLU	VAL
13	GLU	GLY	ASP	THR	HIS	PHE	PRO	ASP	TYR	GLU
14	PRO	ASP	ASP	TRP	GLU	SER	VAL	PHE	SER	GLU
15	PHE	HIS	ASP	ALA	ASP	ALA	GLN	ASN	ALA	HIS
16	SER	TYR	CYS	PHE	GLU	ILE	LEU	GLU	ARG	ARG

1	MET	ILE	SER	LEU	ILE	ALA	ALA	LEU	ALA	VAL
2	ASP	ARG	VAL	ILE	GLY	MET	GLU	ASN	ALA	MET
3	PRO	TRP	PRO	PRO	LEU	PRO	ALA	ASP	LEU	ALA
4	TRP	PHE	LYS	ARG	ASN	THR	LEU	ASN	LYS	PRO
5	VAL	ILE	MET	GLY	ARG	HIS	THR	TRP	GLU	SER
6	ILE	GLY	ARG	PRO	LEU	PRO	GLY	ARG	LYS	ASN
7	ILE	ILE	LEU	SER	SER	GLN	PRO	GLY	THR	ASP
8	ASP	ARG	VAL	THR	TRP	VAL	LYS	SER	VAL	ASP
9	GLU	ALA	ILE	ALA	ALA	CYS	GLY	ASP	VAL	PRO
10	GLU	ILE	MET	VAL	ILE	GLY	GLY	GLY	ARG	VAL
11	TYR	GLU	GLN	PHE	LEU	PRO	LYS	ALA	GLN	LYS
12	LEU	TYR	LEU	THR	HIS	ILE	ASP	ALA	GLU	VAL
13	GLU	GLY	ASP	THR	HIS	PHE	PRO	ASP	TYR	GLU
14	PRO	ASP	ASP	TRP	GLU	SER	VAL	PHE	SER	GLU
15	PHE	HIS	ASP	ALA	ASP	ALA	GLN	ASN	ALA	HIS
16	SER	TYR	CYS	PHE	GLU	ILE	LEU	GLU	ARG	ARG

1	MET	ILE	SER	LEU	ILE	ALA	ALA	LEU	ALA	VAL
2	ASP	ARG	VAL	ILE	GLY	MET	GLU	ASN	ALA	MET
3	PRO	TRP	PRO	PRO	LEU	PRO	ALA	ASP	LEU	ALA
4	TRP	PHE	LYS	ARG	ASN	THR	LEU	ASN	LYS	PRO
5	VAL	ILE	MET	GLY	ARG	HIS	THR	TRP	GLU	SER
6	ILE	GLY	ARG	PRO	LEU	PRO	GLY	ARG	LYS	ASN
7	ILE	ILE	LEU	SER	SER	GLN	PRO	GLY	THR	ASP
8	ASP	ARG	VAL	THR	TRP	VAL	LYS	SER	VAL	ASP
9	GLU	ALA	ILE	ALA	ALA	CYS	GLY	ASP	VAL	PRO
10	GLU	ILE	MET	VAL	ILE	GLY	GLY	GLY	ARG	VAL
11	TYR	GLU	GLN	PHE	LEU	PRO	LYS	ALA	GLN	LYS
12	LEU	TYR	LEU	THR	HIS	ILE	ASP	ALA	GLU	VAL
13	GLU	GLY	ASP	THR	HIS	PHE	PRO	ASP	TYR	GLU
14	PRO	ASP	ASP	TRP	GLU	SER	VAL	PHE	SER	GLU
15	PHE	HIS	ASP	ALA	ASP	ALA	GLN	ASN	ALA	HIS
16	SER	TYR	CYS	PHE	GLU	ILE	LEU	GLU	ARG	ARG