BMRB Entry 25407

Name: Structure of the DNA complex of the C-Terminal domain of MvaT
Published: 2015-06-29

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PDB ID: 2mxf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25407
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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:

Structure of the DNA complex of the C-Terminal domain of MvaT

Deposition date:

2014-12-30

Original release date:

2015-06-29

Authors:

Ding, Pengfei; Xia, Bin

Citation:

Citation: Ding, Pengfei; McFarland, Kirsty; Jin, Shujuan; Tong, Grace; Duan, Bo; Yang, Ally; Hughes, Timothy; Liu, Jun; Dove, Simon; Navarre, William; Xia, Bin. "A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT" Plos Pathog. 11, e1004967-e1004967 (2015).
PubMed: 26068099

Assembly members:

Assembly members:
MvaT, polymer, 55 residues, 5352.173 Da.
DNA_(5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'), polymer, 12 residues, 3662.434 Da.

Natural source:

Natural source: Common Name: Pseudomonas aeruginosa Taxonomy ID: 287 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas aeruginosa

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MvaT: MKRARKVKQYKNPHTGEVIE TKGGNHKTLKEWKAKWGPEA VESWATLLGHHHHHH
DNA_(5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'): CGCATATATGCG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	163
15N chemical shifts	51
1H chemical shifts	536

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MvaT	1
2	DNA (5'-D(CPGPCPAPTPAPTPAPTPGPCPG)-3')_1	2
3	DNA (5'-D(CPGPCPAPTPAPTPAPTPGPCPG)-3')_2	2

Entities:

Entity 1, MvaT 55 residues - 5352.173 Da.

1

MET

LYS

ARG

ALA

ARG

LYS

VAL

LYS

GLN

TYR

2

LYS

ASN

PRO

HIS

THR

GLY

GLU

VAL

ILE

GLU

3

THR

LYS

GLY

ASN

HIS

LYS

THR

LEU

LYS

4

GLU

TRP

LYS

ALA

LYS

TRP

GLY

PRO

GLU

ALA

5

VAL

GLU

SER

TRP

ALA

THR

LEU

GLY

HIS

6

HIS

Entity 2, DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3')_1 12 residues - 3662.434 Da.

1

DC

DG

DC

DA

DT

DA

DT

DA

DT

DG

2

DC

DG

Samples:

sample_1: MvaT, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 50 mM; sodium chloride 50 mM; DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3') 1 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz

BMRB	25405
PDB	2MXE 2MXF
DBJ	BAK88160 BAP21250 BAP52811 BAQ41953 BAR69621
EMBL	CAW29447 CCQ87551 CDH72901 CDH79198 CDI92830
GB	AAG07703 AAP33788 ABJ13585 ABR84836 AEO76886
REF	NP_253005 WP_003093888 WP_003125172 WP_012077126 WP_015478773