BMRB Entry 19510

Name: NMR structure of the Paracoccus denitrificans Z-subunit determined in the presence of ADP
Published: 2013-10-08

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PDB ID: 2mdz
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/BMR19510
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the Paracoccus denitrificans Z-subunit determined in the presence of ADP

Deposition date:

2013-09-20

Original release date:

2013-10-08

Authors:

Serrano, Pedro; Geralt, Michael; Wuthrich, Kurt; Morales-Rios, Edga; Zarco-Zavala, Mariel; Garcia-Trejo, Jose; Dutta, Samit; JCSG, JCSG

Citation:

Citation: Serrano, Pedro; Geralt, Michael; Wuthrich, Kurt; Dutta, Samit; Morales-Rios, Edga; Garcia-Trejo, Jose; Zarco-Zavala, Mariel. "NMR structure of the putative ATPase regulatory protein YP_916642.1 from Paracoccus denitrificans" .

Assembly members:

Assembly members:
Z-subunit, polymer, 104 residues, 11687.060 Da.
ADENOSINE-5'-DIPHOSPHATE, non-polymer, 427.201 Da.

Natural source:

Natural source: Common Name: alpha proteobacteria Taxonomy ID: 266 Superkingdom: Bacteria Kingdom: not available Genus/species: Paracoccus denitrificans

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Z-subunit: MTTFDDRERAHEAKFAHDAE LNFKAEARRNRLLGEWAAGL LGKTGDDARAYALTVVTSDF DEPGDEDVFRKLAADLEGKA DEETIRAKMVELRATAREQI ISEI

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	381
15N chemical shifts	103
1H chemical shifts	624

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Z-subunit	1
2	ADP	2

Entities:

Entity 1, Z-subunit 104 residues - 11687.060 Da.

1

MET

THR

PHE

ASP

ARG

GLU

ARG

ALA

2

HIS

GLU

ALA

LYS

PHE

ALA

HIS

ASP

ALA

GLU

3

LEU

ASN

PHE

LYS

ALA

GLU

ALA

ARG

ASN

4

ARG

LEU

GLY

GLU

TRP

ALA

GLY

LEU

5

LEU

GLY

LYS

THR

GLY

ASP

ALA

ARG

ALA

6

TYR

ALA

LEU

THR

VAL

THR

SER

ASP

PHE

7

ASP

GLU

PRO

GLY

ASP

GLU

ASP

VAL

PHE

ARG

8

LYS

LEU

ALA

ASP

LEU

GLU

GLY

LYS

ALA

9

ASP

GLU

THR

ILE

ARG

ALA

LYS

MET

VAL

10

GLU

LEU

ARG

ALA

THR

ALA

ARG

GLU

GLN

ILE

11

ILE

SER

GLU

ILE

Entity 2, ADP - 427.201 Da.

1

ADP

Samples:

sample_1: Z-subunit, [U-98% 13C; U-98% 15N], 1.5 mM; sodium chloride 50 mM; sodium phosphate 25 mM; sodium azide 5 mM; ADP 10 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.083 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
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
5D APSY CBCACONH	sample_1	isotropic	sample_conditions_1
4D APSY HACANH	sample_1	isotropic	sample_conditions_1
5D APSY HACACONH	sample_1	isotropic	sample_conditions_1

Software:

DYANA - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

BMRB	18018
PDB	2LL0 2MDZ 5DN6
GB	ABL70946
REF	WP_011749137