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BMRB: 36061

5X5S

Ligand induced structure of AmyP-SBD

Authors

Li, X., Yu, J., Sun, H., Zhang, X.

Assembly

AmyP-SBD

Entity

1. AmyP-SBD (polymer, Thiol state: all disulfide bound), 157 monomers, 17002.69 Da Detail

TPSASGLTKV ATVSAASSLI GEGFMAQCDN PTIEGDGPIG KTLYVVGDFA DASWKQKPHR AYRYVGENTY QAVVDEKAGA FRMQYASKDW SPQFTADGLE LTPGKTASLK RGGYGQDTAV TLPEAGQYVW SLKFTDSGDP EQIMVSKCPL EHHHHHH

Formula weight

17002.69 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS28:SG	1:CYS148:SG

Source organism

uncultured bacterium

Exptl. method

solution NMR

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 83.4 %, Completeness (bb): 90.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.4 % (1455 of 1745)	86.4 % (776 of 898)	77.1 % (529 of 686)	93.2 % (150 of 161)
Backbone	90.8 % (839 of 924)	92.2 % (296 of 321)	89.0 % (405 of 455)	93.2 % (138 of 148)
Sidechain	77.1 % (742 of 962)	83.2 % (480 of 577)	67.2 % (250 of 372)	92.3 % (12 of 13)
Aromatic	30.0 % (51 of 170)	52.9 % (45 of 85)	4.9 % (4 of 82)	66.7 % (2 of 3)
Methyl	88.5 % (131 of 148)	93.2 % (69 of 74)	83.8 % (62 of 74)

1. entity 1

TPSASGLTKV ATVSAASSLI GEGFMAQCDN PTIEGDGPIG KTLYVVGDFA DASWKQKPHR AYRYVGENTY QAVVDEKAGA FRMQYASKDW SPQFTADGLE LTPGKTASLK RGGYGQDTAV TLPEAGQYVW SLKFTDSGDP EQIMVSKCPL EHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 15N] AmyP-SBD, 2 mM NA- beta-cyclodextrin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	AmyP-SBD	[U-99% 15N]	protein	0.4 mM
2	beta-cyclodextrin	natural abundance		2 mM
3	NaH2PO4	natural abundance	buffer	20 mM
4	NaCl	natural abundance	salt	150 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 13C; U-99% 15N] AmyP-SBD, 2 mM NA beta-cyclodextrin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 13C; U-99% 15N] AmyP-SBD, 2 mM NA beta-cyclodextrin, 100% D2O

#	Name	Isotope labeling	Type	Concentration
11	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
12	beta-cyclodextrin	natural abundance		2 mM
13	D2O	[U-2H]	solvent	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: 0.65 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5X5S, Strand ID: A Detail

Release date

2017-04-18

Citation

Ligand induced folding of the first identified CBM69 starch binding domain AmyP-SBD
Li, X., Yu, J., Tu, X., Sun, H., Peng, H., Zhang, X.
Protein Pept. Lett. (2018), PubMed 29359648 , DOI 10.2174/0929866525666180122145846 , Abstract

Related entities 1. AmyP-SBD, : 1 : 2 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 15N] AmyP-SBD, 2 mM NA- beta-cyclodextrin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	AmyP-SBD	[U-99% 15N]	protein	0.4 mM
2	beta-cyclodextrin	natural abundance		2 mM
3	NaH2PO4	natural abundance	buffer	20 mM
4	NaCl	natural abundance	salt	150 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

2 3D 1H-15N TOCSY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 15N] AmyP-SBD, 2 mM NA- beta-cyclodextrin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	AmyP-SBD	[U-99% 15N]	protein	0.4 mM
2	beta-cyclodextrin	natural abundance		2 mM
3	NaH2PO4	natural abundance	buffer	20 mM
4	NaCl	natural abundance	salt	150 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

3 3D 1H-15N NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 15N] AmyP-SBD, 2 mM NA- beta-cyclodextrin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	AmyP-SBD	[U-99% 15N]	protein	0.4 mM
2	beta-cyclodextrin	natural abundance		2 mM
3	NaH2PO4	natural abundance	buffer	20 mM
4	NaCl	natural abundance	salt	150 mM
5	H2O	natural abundance	solvent	90 %
6	D2O	[U-2H]	solvent	10 %

4 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-99% 13C; U-99% 15N] AmyP-SBD, 2 mM NA beta-cyclodextrin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

5 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

6 3D CBCANH

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

7 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

8 3D HCC(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

9 3D CC(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

10 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

11 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

12 3D HNCA

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

13 3D HN(CO)CA

Instrument

Bruker DMX - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	AmyP-SBD	[U-99% 13C; U-99% 15N]	protein	0.4 mM
8	beta-cyclodextrin	natural abundance		2 mM
9	H2O	natural abundance	solvent	90 %
10	D2O	[U-2H]	solvent	10 %

14 3D HCCH-TOCSY