BMRB Entry 25693

Name: Solution structure of a disulfide stabilized XCL1 dimer
Published: 2015-10-05

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PDB ID: 2n54
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25693
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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 a disulfide stabilized XCL1 dimer PubMed: 26302421

Deposition date: 2015-07-07 Original release date: 2015-10-05

Authors: Tyler, Robert; Tuinstra, Robbyn; Peterson, Francis; Volkman, Brian

Citation: Fox, Jamie; Tyler, Robert; Guzzo, Christina; Tuinstra, Robbyn; Peterson, Francis; Lusso, Paolo; Volkman, Brian. "Engineering Metamorphic Chemokine Lymphotactin/XCL1 into the GAG-Binding, HIV-Inhibitory Dimer Conformation" ACS Chem. Biol. 10, 2580-2588 (2015).

Assembly members:
XCL1, polymer, 93 residues, 10271.7 Da.

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
XCL1: VGSEVSDKRTCVSLTTQRLP VSRIKTYTITEGSLRCVIFI TKRGLKVCCDPQATWVRDVV RSMDRKSNTRNNMIQTKPTG TQQSTNTAVTLTG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	257
15N chemical shifts	62
1H chemical shifts	397

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_2	1

Entities:

Entity 1, entity_1 93 residues - 10271.7 Da.

1

VAL

GLY

SER

GLU

VAL

SER

ASP

LYS

ARG

THR

2

CYS

VAL

SER

LEU

THR

GLN

ARG

LEU

PRO

3

VAL

SER

ARG

ILE

LYS

THR

TYR

THR

ILE

THR

4

GLU

GLY

SER

LEU

ARG

CYS

VAL

ILE

PHE

ILE

5

THR

LYS

ARG

GLY

LEU

LYS

VAL

CYS

ASP

6

PRO

GLN

ALA

THR

TRP

VAL

ARG

ASP

VAL

7

ARG

SER

MET

ASP

ARG

LYS

SER

ASN

THR

ARG

8

ASN

MET

ILE

GLN

THR

LYS

PRO

THR

GLY

9

THR

GLN

SER

THR

ASN

THR

ALA

VAL

THR

10

LEU

THR

GLY

Samples:

sample_1: XCL1, [U-99% 13C; U-99% 15N], 1 mM; potassium phosphate 20 mM; sodium azide, [U-100% 15N], 0.02%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.0; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D F1-13C/F3-13C edited NOESY	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

XEASY, Bartels et al. - data analysis

GARANT, Bartels, Guntert, Billeter and Wuthrich - chemical shift assignment

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization

NMR spectrometers:

Bruker DRX 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts