BMRB Entry 18477

Name: NMR dynamics in the C-terminal globular domain of oligosaccharyltransferase
Published: 2012-11-26

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18477

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR dynamics in the C-terminal globular domain of oligosaccharyltransferase

Deposition date:

2012-05-23

Original release date:

2012-11-26

Authors:

Nyirenda, James; Matsumoto, Shunsuke; Takashi, Saitoh; Kohda, Daisuke

Citation:

Citation: Nyirenda, James; Matsumoto, Shunsuke; Saitoh, Takashi; Maita, Nobuo; Noda, Nobuo; Inagaki, Fuyuhiko; Kohda, Daisuke. "Crystallographic and NMR evidence for flexibility in oligosaccharyltransferases and its catalytic significance." Structure 21, 32-41 (2013).
PubMed: 23177926

Assembly members:

Assembly members:
AfAglB-S2, polymer, 180 residues, Formula weight is not available

Natural source:

Natural source: Common Name: euryarchaeotes Taxonomy ID: 2234 Superkingdom: Archae Kingdom: not available Genus/species: Archaeoglobus fulgidus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET47b+

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AfAglB-S2: MAHHHHHHSAALEVLFQGPE MTMDWKEALNWMKENLEAQD YLKAYEKPDYAVLSWWDYGN WILYVAKKAVVCNNFQAGAD DAAKFFTAQSEEEAMKIVEK RKVRYVVTVEELTVKPETNK TKFIPIMQIAGYSPEYMKNK EIIDFFNKTMLYKLHVENAT NLTHFRLLKNFGTVKIFEVK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
- heteronuclear_noe_list_2
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
- heteronuclear_T1_list_2
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
- heteronuclear_T2_list_2
order_parameters
- order_parameter_list_1

Data type	Count
15N chemical shifts	151
1H chemical shifts	151
heteronuclear NOE values	264
order parameters	130
T1 relaxation values	264
T2 relaxation values	264

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AfAglB-S2	1

Entities:

Entity 1, AfAglB-S2 180 residues - Formula weight is not available

Residues 1-19 are plasmid derived and part of the sequence in the assigned residues is labeled 10-18 from Alanine number 10 and the target sequence starts from 433.

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

Samples:

sample_1: AfAglB-S2, [U-99% 13C; U-99% 15N], 1.0 mM; AfAglB-S2, [U-99% 15N], 1.0 mM; H2O 90%; D2O 10%

Sample_2: AfAglB-S2, [U-99% 15N], 0.5-1.0 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 5 mM; pH: 7.0; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
1H-15N heteronuclear noe	Sample_2	isotropic	sample_conditions_2
1H-15N heteronuclear noe	Sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	Sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	Sample_2	isotropic	sample_conditions_2

Software:

TOPSPIN v2, Bruker Biospin - collection

NMRPipe, Delaglio, Zhengrong and Bax - processing

SPARKY, Goddard - chemical shift assignment

ModelFree v4.16, Palmer - data analysis

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz

GB	AAB91198
REF	WP_048064157

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

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