BMRB Entry 50261

Name: Vitronectin hemopexin-like domain with DHPC
Published: 2020-07-01

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50261

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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:

Vitronectin hemopexin-like domain with DHPC

Deposition date:

2020-05-05

Original release date:

2020-07-01

Authors:

Shin, Kyungsoo; Kent, James; Singh, Chandan; Fujimoto, Lynn; Yu, Jinghua; Tian, Ye; Im, Wonpil; Marassi, Francesca

Citation:

Citation: Shin, Kyungsoo; Kent, James; Singh, Chandan; Fujimoto, Lynn; Yu, Jinghua; Tian, Ye; Im, Wonpil; Marassi, Francesca. "Calcium and hydroxyapatite binding site of human vitronectin provides new insights to abnormal deposit formation" Proc. Natl. Acad. Sci. U.S.A. 117, 18504-18510 (2020).
PubMed: 32699145

Assembly members:

Assembly members:
entity_1, polymer, 204 residues, Formula weight is not available

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 Vector: pET23a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MELCSGKPFDAFTDLKNGSL FAFRGQYSYELDEKAVRPGY PKLIRDVWGIEGPIDAAFTR INSQGKTYLFKGSQYWRFED GVLDPDYPRNISDGFDGIPD NVDAALALPAHSYSGRERVY FFKGKQYWEYQFQRTSAGTR QPQFISRDWHGVPGQVDAAM AGRISVFFFSGDKYYRVNLR TRRVDTVDPPYPRSIAQYWL GCPA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	514
15N chemical shifts	174
1H chemical shifts	174

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Vitronectin hemopexin-like domain	1

Entities:

Entity 1, Vitronectin hemopexin-like domain 204 residues - Formula weight is not available

1

MET

GLU

LEU

CYS

SER

GLY

LYS

PRO

PHE

ASP

2

ALA

PHE

THR

ASP

LEU

LYS

ASN

GLY

SER

LEU

3

PHE

ALA

PHE

ARG

GLY

GLN

TYR

SER

TYR

GLU

4

LEU

ASP

GLU

LYS

ALA

VAL

ARG

PRO

GLY

TYR

5

PRO

LYS

LEU

ILE

ARG

ASP

VAL

TRP

GLY

ILE

6

GLU

GLY

PRO

ILE

ASP

ALA

PHE

THR

ARG

7

ILE

ASN

SER

GLN

GLY

LYS

THR

TYR

LEU

PHE

8

LYS

GLY

SER

GLN

TYR

TRP

ARG

PHE

GLU

ASP

9

GLY

VAL

LEU

ASP

PRO

ASP

TYR

PRO

ARG

ASN

10

ILE

SER

ASP

GLY

PHE

ASP

GLY

ILE

PRO

ASP

11

ASN

VAL

ASP

ALA

LEU

ALA

LEU

PRO

ALA

12

HIS

SER

TYR

SER

GLY

ARG

GLU

ARG

VAL

TYR

13

PHE

LYS

GLY

LYS

GLN

TYR

TRP

GLU

TYR

14

GLN

PHE

GLN

ARG

THR

SER

ALA

GLY

THR

ARG

15

GLN

PRO

GLN

PHE

ILE

SER

ARG

ASP

TRP

HIS

16

GLY

VAL

PRO

GLY

GLN

VAL

ASP

ALA

MET

17

ALA

GLY

ARG

ILE

SER

VAL

PHE

SER

18

GLY

ASP

LYS

TYR

ARG

VAL

ASN

LEU

ARG

19

THR

ARG

VAL

ASP

THR

VAL

ASP

PRO

20

TYR

PRO

ARG

SER

ILE

ALA

GLN

TYR

TRP

LEU

21

GLY

CYS

PRO

ALA

Samples:

sample_1: Vitronectin hemopexin-like domain, [U-100% 13C; U-100% 15N], 90 uM; MES 20 mM; NaCl 300 mM; DHPC 4.5 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 303.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v2.4.2 - chemical shift assignment, data analysis, peak picking

TALOS-N - data analysis

TOPSPIN - collection, processing

NMR spectrometers:

Bruker Avance 600 MHz

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