BMRB Entry 25312

Name: SOLUTION STRUCTURE OF HUMAN MBD1 CXXC1 DOMAIN
Published: 2015-09-21

Click here to enlarge.

PDB ID: 4d4w
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25312
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

SOLUTION STRUCTURE OF HUMAN MBD1 CXXC1 DOMAIN

Deposition date:

2014-11-03

Original release date:

2015-09-21

Authors:

Thomson, Ross; Smith, Brian

Citation:

Citation: Thomson, Ross; Smith, Brian. "Solution structure of human MBD1 CXXC1" J. Biomol. NMR 63, 309-314 (2015).
PubMed: 26354109

Assembly members:

Assembly members:
MBD1_CXXC1, polymer, 61 residues, 6673.7301 Da.
entity_ZN, non-polymer, 65.409 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: pGEX-6P1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MBD1_CXXC1: GPLGSEQRMFKRVGCGECAA CQVTEDCGACSTCLLQLPHD VASGLFCKCERRRCLRIVER S

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list
heteronucl_T1_relaxation
- heteronuclear_T1_list
heteronucl_T2_relaxation
- heteronuclear_T2_list
spectral_peak_list

Data type	Count
15N chemical shifts	62
1H chemical shifts	344
T1 relaxation values	55
T2 relaxation values	53

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MBD1 CXXC1	1
2	ZINC ION	2

Entities:

Entity 1, MBD1 CXXC1 61 residues - 6673.7301 Da.

1

GLY

PRO

LEU

GLY

SER

GLU

GLN

ARG

MET

PHE

2

LYS

ARG

VAL

GLY

CYS

GLY

GLU

CYS

ALA

3

CYS

GLN

VAL

THR

GLU

ASP

CYS

GLY

ALA

CYS

4

SER

THR

CYS

LEU

GLN

LEU

PRO

HIS

ASP

5

VAL

ALA

SER

GLY

LEU

PHE

CYS

LYS

CYS

GLU

6

ARG

CYS

LEU

ARG

ILE

VAL

GLU

ARG

7

SER

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

MBD1_CXXC1_1: MBD1_CXXC1, [U-15N], 1.0 mM; NaCl 250.0 mM; tris(hydroxymethyl)aminomethane 10.0 mM

sample_new_1: MBD1_CXXC1, [U-13C; U-15N], 0.0010000 M; NaCl 250.0 mM; tris(hydroxymethyl)aminomethane 10.0 mM

MBD1_CXXC1_2: ionic strength: 0.250 M; pH: 7.500; pressure: 1.000 atm; temperature: 293.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
2D 1H-1H TOCSY	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
2D 1H-15N HSQC/HMQC	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
3D 1H-15N TOCSY	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
2D 1H-1H NOESY	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
2D 1H-1H NOESY	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
3D 1H-15N NOESY	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
T2 (H[n[T2(N)]])	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
T1 (H[n[T1(N)]])	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
HNHA (H{[N]+[HA]})	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
3D HNHB	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
2D 1H-15N HSQC/HMQC	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
2D 1H-15N HSQC/HMQC	MBD1_CXXC1_1	isotropic	MBD1_CXXC1_2
HNHB	sample_new_1	solution	MBD1_CXXC1_2

Software:

ARIA v2.3, Bioinformatique Structurale - structure calculation

AutoDep v4.3, PDBe - collection

CCPNMR_Analysis v1.0, CCPN - assignment of spectra

CNS v1.2, BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARREN - Structure calculation

Topsin v1.3, Bruker - data collection

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz
Bruker AVANCE 600 MHz

UNP	MBD1_HUMAN
AlphaFold	Q9UNZ9