BMRB Entry 34352

Name: Solution NMR ensemble for a chimeric KH-S1 domain construct of exosomal polynucleotide phosphrylase at 298K compiled using the CoMAND method
Published: 2019-10-03

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PDB ID: 6qh2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34352
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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 NMR ensemble for a chimeric KH-S1 domain construct of exosomal polynucleotide phosphrylase at 298K compiled using the CoMAND method

Deposition date:

2019-01-14

Original release date:

2019-10-03

Authors:

ElGamacy, M.; Truffault, V.; Zhu, H.; Coles, M.

Citation:

Citation: ElGamacy, M.; Riss, M.; Zhu, H.; Truffault, V.; Coles, M.. "Mapping Local Conformational Landscapes of Proteins in Solution." Structure 27, 853-865 (2019).
PubMed: 30930065

Assembly members:

Assembly members:
entity_1, polymer, 171 residues, 18396.865 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 409438 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: GAMGRGDISEFAPRIHTIKI NPDKIKDVIGKGGSVIRALT EETGTTIEIEDDGTVKIAAT DGEKAKHAIRRIEEITAEIE VGRVYTGKVTRIVDFGAFVA IGGGKEGLVHISQIADKRVE KVTDYLQMGQEVPVKVLEVD RQGRIRLSIKEATEQSQPAA APEAPAAEQGE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	599
15N chemical shifts	133
1H chemical shifts	708

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 171 residues - 18396.865 Da.

1

GLY

ALA

MET

GLY

ARG

GLY

ASP

ILE

SER

GLU

2

PHE

ALA

PRO

ARG

ILE

HIS

THR

ILE

LYS

ILE

3

ASN

PRO

ASP

LYS

ILE

LYS

ASP

VAL

ILE

GLY

4

LYS

GLY

SER

VAL

ILE

ARG

ALA

LEU

THR

5

GLU

THR

GLY

THR

ILE

GLU

ILE

GLU

6

ASP

GLY

THR

VAL

LYS

ILE

ALA

THR

7

ASP

GLY

GLU

LYS

ALA

LYS

HIS

ALA

ILE

ARG

8

ARG

ILE

GLU

ILE

THR

ALA

GLU

ILE

GLU

9

VAL

GLY

ARG

VAL

TYR

THR

GLY

LYS

VAL

THR

10

ARG

ILE

VAL

ASP

PHE

GLY

ALA

PHE

VAL

ALA

11

ILE

GLY

LYS

GLU

GLY

LEU

VAL

HIS

12

ILE

SER

GLN

ILE

ALA

ASP

LYS

ARG

VAL

GLU

13

LYS

VAL

THR

ASP

TYR

LEU

GLN

MET

GLY

GLN

14

GLU

VAL

PRO

VAL

LYS

VAL

LEU

GLU

VAL

ASP

15

ARG

GLN

GLY

ARG

ILE

ARG

LEU

SER

ILE

LYS

16

GLU

ALA

THR

GLU

GLN

SER

GLN

PRO

ALA

17

ALA

PRO

GLU

ALA

PRO

ALA

GLU

GLN

GLY

18

GLU

Samples:

sample_1: KH-S1, [U-99% 13C; U-99% 15N], 1.6 mM; potassium phosphate 50 mM; sodium chloride 125 mM; HOPES buffer 25 mM

sample_conditions_1: ionic strength: 125 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 C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D CNH-NOESY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

Sparky, Goddard - chemical shift assignment

Shine, Riss & Coles - structure calculation

Rosetta v3.6, Das & Baker - structure calculation

NAMD v2.12, University of Illinois - refinement

CoMAND, in house - refinement

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 800 MHz

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