BMRB Entry 26045

Name: Solution structure of the de novo mini protein HHH_06
Published: 2016-09-13

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PDB ID: 2nd2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR26045
MolProbity Validation Chart

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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:

Solution structure of the de novo mini protein HHH_06

Deposition date:

2016-04-22

Original release date:

2016-09-13

Authors:

Eletsky, Alexander; Bahl, Christopher; Gilmore, Jason; Buchko, Garry; Baker, David

Citation:

Citation: Bhardwaj, G.; Mulligan, V.; Bahl, C.; Gilmore, J.; Harvey, P.; Cheneval, O.; Buchko, G.; Pulavarti, S.; Kaas, Q.; Eletsky, A.; Huang, P.; Johnsen, W.; Greisen, P.; Rocklin, G.; Song, Y.; Linsky, T.; Watkins, A.; Rettie, S.; Xu, X.; Carter, L.; Bonneau, R.; Olson, J.; Coutsias, E.; Correnti, C.; Szyperski, T.; Craik, D.; Baker, D.. "Accurate de novo design of hyperstable constrained peptides." Nature 538, 329-335 (2016).
PubMed: 27626386

Assembly members:

Assembly members:
HHH_06, polymer, 44 residues, 5119.8 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pet15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HHH_06: APCEDLKERLKKLGMSEECR QRLEKMCKEGTSEDAERMAR NCES

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	155
15N chemical shifts	49
1H chemical shifts	303

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HHH_06	1

Entities:

Entity 1, HHH_06 44 residues - 5119.8 Da.

1

ALA

PRO

CYS

GLU

ASP

LEU

LYS

GLU

ARG

LEU

2

LYS

LEU

GLY

MET

SER

GLU

CYS

ARG

3

GLN

ARG

LEU

GLU

LYS

MET

CYS

LYS

GLU

GLY

4

THR

SER

GLU

ASP

ALA

GLU

ARG

MET

ALA

ARG

5

ASN

CYS

GLU

SER

Samples:

sample_1: sodium phosphate 50 mM; DSS 4 uM; D2O, [U-99% 2H], 10%; sodium azide 0.02%; HHH_06, [U-100% 15N], 1 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H DPFGSE TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H DPFGSE NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY HSQC	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1

Software:

vnmrj, Varian - collection

prosa, Guntert - processing

xeasy, Bartels et al. - data analysis

cara, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

cyana, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

pdbstat, pdbstat (Moseley, Montelione) - data analysis

PSVS, Bhattacharya and Montelione - RPF calculation, validation, violations

NMR spectrometers:

Agilent DD2 600 MHz
Varian INOVA 750 MHz

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