BMRB Entry 30186

Name: NMR structure of holo-PS1
Published: 2017-08-03

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PDB ID: 5tgy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30186
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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:

NMR structure of holo-PS1

Deposition date:

2016-09-28

Original release date:

2017-08-03

Authors:

Polizzi, N.; Wu, Y.

Citation:

Citation: Polizzi, Nicholas; Wu, Yibing; Lemmin, Thomas; Maxwell, Alison; Zhang, Shao-Qing; Rawson, Jeff; Beratan, David; Therien, Michael; DeGrado, William. "De novo design of a hyperstable non-natural protein-ligand complex with sub-angstrom accuracy." Nat. Chem. 9, 1157-1164 (2017).
PubMed: 29168496

Assembly members:

Assembly members:
entity_1, polymer, 109 residues, 12965.262 Da.
entity_7BU, non-polymer, 645.737 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SEFEKLRQTGDELVQAFQRL REIFDKGDDDSLEQVLEEIE ELIQKHRQLFDNRQEAADTE AAKQGDQWVQLFQRFREAID KGDKDSLEQLLEELEQALQK IRELAEKKN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	377
15N chemical shifts	129
1H chemical shifts	820

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_7BU	2

Entities:

Entity 1, entity_1 109 residues - 12965.262 Da.

1

SER

GLU

PHE

GLU

LYS

LEU

ARG

GLN

THR

GLY

2

ASP

GLU

LEU

VAL

GLN

ALA

PHE

GLN

ARG

LEU

3

ARG

GLU

ILE

PHE

ASP

LYS

GLY

ASP

4

SER

LEU

GLU

GLN

VAL

LEU

GLU

ILE

GLU

5

GLU

LEU

ILE

GLN

LYS

HIS

ARG

GLN

LEU

PHE

6

ASP

ASN

ARG

GLN

GLU

ALA

ASP

THR

GLU

7

ALA

LYS

GLN

GLY

ASP

GLN

TRP

VAL

GLN

8

LEU

PHE

GLN

ARG

PHE

ARG

GLU

ALA

ILE

ASP

9

LYS

GLY

ASP

LYS

ASP

SER

LEU

GLU

GLN

LEU

10

LEU

GLU

LEU

GLU

GLN

ALA

LEU

GLN

LYS

11

ILE

ARG

GLU

LEU

ALA

GLU

LYS

ASN

Entity 2, entity_7BU - C24 H8 F12 N4 Zn - 645.737 Da.

1

7BU

Samples:

sample_1: holo-PS1, [U-100% 13C; U-100% 15N], 780 uM; NaCl 100 mM; NaPi 50 mM

sample_2: holo-PS1, [U-10% 13C; U-100% 15N], 780 uM; NaCl 100 mM; NaPi 50 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CO(CA)NH	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D simultaneous NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

XEASY, Bartels et al. - peak picking

NMR spectrometers:

Bruker AvanceII 900 MHz

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