BMRB Entry 52678

Name: NMR solution structure of human matrix Gla protein
Published: 2025-01-03

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52678

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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 solution structure of human matrix Gla protein

Deposition date:

2024-11-06

Original release date:

2025-01-03

Authors:

Lau, Yee Shun; Sharpe, Simon

Citation:

Citation: Lau, Yee Shun; Sharpe, Simon. "Dynamic Structure of Human Matrix Gla Protein Revealed by Solution NMR" Protein Sci. ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 84 residues, 10412.65 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: YESHESMESYELNPFINRRN ANTFISPQQRWRAKVQERIR ERSKPVHELNREACDDYRLC ERYAMVYGYNAAYNRYFRKR RGTK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	378
15N chemical shifts	80
1H chemical shifts	553

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Human matrix Gla protein	1

Entities:

Entity 1, Human matrix Gla protein 84 residues - 10412.65 Da.

This is the mature peptide of human matrix Gla protein, excluding the signal peptide.

1

TYR

GLU

SER

HIS

GLU

SER

MET

GLU

SER

TYR

2

GLU

LEU

ASN

PRO

PHE

ILE

ASN

ARG

ASN

3

ALA

ASN

THR

PHE

ILE

SER

PRO

GLN

ARG

4

TRP

ARG

ALA

LYS

VAL

GLN

GLU

ARG

ILE

ARG

5

GLU

ARG

SER

LYS

PRO

VAL

HIS

GLU

LEU

ASN

6

ARG

GLU

ALA

CYS

ASP

TYR

ARG

LEU

CYS

7

GLU

ARG

TYR

ALA

MET

VAL

TYR

GLY

TYR

ASN

8

ALA

TYR

ASN

ARG

TYR

PHE

ARG

LYS

ARG

9

ARG

GLY

THR

LYS

Samples:

sample_1: Human matrix Gla protein, [U-13C; U-15N], 520 uM; Boric acid 50 mM; D2O 10%

sample_2: Human matrix Gla protein, [U-13C; U-15N], 567 uM; Boric acid 50 mM; D2O 10%

sample_conditions_1: pH: 5.7; pressure: 1 atm; temperature: 279.92 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
T1/R1 relaxation	sample_1	isotropic	sample_conditions_1
T2/R2 relaxation	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_2	isotropic	sample_conditions_1
3D CBCANH	sample_2	isotropic	sample_conditions_1
3D (H)CC(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)N(CA)NNH	sample_2	isotropic	sample_conditions_1
3D (H)N(COCA)NNH	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	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

Software:

TOPSPIN v3.2 - collection

CcpNMR v2.5.2 - chemical shift assignment, data analysis, peak picking

CcpNMR v3.2.5 - chemical shift assignment, data analysis, peak picking

NMRPipe v11.5 - processing

NMRDraw v11.5 - processing

PONDEROSA-C/S vBuild: 2020/01/21 - refinement, structure solution

PDBStat v5.24.031 - Conversion of restraint files from Ponderosa Calculation to NEF format for PDB deposition., data analysis

POKY vBuild: 11/27/2023r - refinement, structure solution

NMR spectrometers:

Bruker AVANCE III 600 MHz

NCBI	AAB53765.1
UniProtKB/Swiss-Prot	P08493