BMRB Entry 17595

Name: NMR resonance assignments for an archaeal homolog of the endonuclease Nob1 involved in ribosome biogenesis
Published: 2011-12-14

Click here to enlarge.

PDB ID: 2lcq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17595
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:

NMR resonance assignments for an archaeal homolog of the endonuclease Nob1 involved in ribosome biogenesis

Deposition date:

2011-04-19

Original release date:

2011-12-14

Authors:

Veith, Thomas; Wurm, Jan; Duchardt-Ferner, Elke; Weis, Benjamin; Hennig, Raoul; Martin, Roman; Safferthal, Charlotta; Bohnsack, Markus; Schleiff, Enrico; Woehnert, Jens

Citation:

Citation: Veith, Thomas; Martin, Roman; Wurm, Jan; Weis, Benjamin; Duchardt-Ferner, Elke; Safferthal, Charlotta; Hennig, Raoul; Mirus, Oliver; Bohnsack, Markus; Wohnert, Jens; Schleiff, Enrico. "Structural and functional analysis of the archaeal endonuclease Nob1." Nucleic Acids Res. 40, 3259-3274 (2012).
PubMed: 22156373

Assembly members:

Assembly members:
PhNob1, polymer, 161 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Euryarchaeotes Taxonomy ID: 53953 Superkingdom: Archaea Kingdom: not available Genus/species: Pyrococcus horikoshii

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PhNob1: MLRNLKKTLVLDSSVFIQGI DIEGYTTPSVVEEIKDRESK IFLESLISAGKVKIAEPSKE SIDRIIQVAKETGEVNELSK ADIEVLALAYELKGEIFSDD YNVQNIASLLGLRFRTLKRG IKKVIKWRYVCIGCGRKFST LPPGGVCPDCGSKVKLIPRK R

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	704
15N chemical shifts	160
1H chemical shifts	1097

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PhNob1	1
2	Zn	2

Entities:

Entity 1, PhNob1 161 residues - Formula weight is not available

1

MET

LEU

ARG

ASN

LEU

LYS

THR

LEU

VAL

2

LEU

ASP

SER

VAL

PHE

ILE

GLN

GLY

ILE

3

ASP

ILE

GLU

GLY

TYR

THR

PRO

SER

VAL

4

VAL

GLU

ILE

LYS

ASP

ARG

GLU

SER

LYS

5

ILE

PHE

LEU

GLU

SER

LEU

ILE

SER

ALA

GLY

6

LYS

VAL

LYS

ILE

ALA

GLU

PRO

SER

LYS

GLU

7

SER

ILE

ASP

ARG

ILE

GLN

VAL

ALA

LYS

8

GLU

THR

GLY

GLU

VAL

ASN

GLU

LEU

SER

LYS

9

ALA

ASP

ILE

GLU

VAL

LEU

ALA

LEU

ALA

TYR

10

GLU

LEU

LYS

GLY

GLU

ILE

PHE

SER

ASP

11

TYR

ASN

VAL

GLN

ASN

ILE

ALA

SER

LEU

12

GLY

LEU

ARG

PHE

ARG

THR

LEU

LYS

ARG

GLY

13

ILE

LYS

VAL

ILE

LYS

TRP

ARG

TYR

VAL

14

CYS

ILE

GLY

CYS

GLY

ARG

LYS

PHE

SER

THR

15

LEU

PRO

GLY

VAL

CYS

PRO

ASP

CYS

16

GLY

SER

LYS

VAL

LYS

LEU

ILE

PRO

ARG

LYS

17

ARG

Entity 2, Zn - Zn - 65.409 Da.

1

ZN

Samples:

15N: PhNob1, [U-15N], 0.4 mM; potassium chloride 50 mM; BisTris 50 mM; H2O 90%; D2O 10%

sample_1: PhNob1, [U-13C; U-15N], 0.4 mM; potassium chloride 50 mM; BisTris 50 mM; H2O 90%; D20 10%

sample_conditions_1: ionic strength: 83 mM; pH: 6.2; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNHA	15N	isotropic	sample_conditions_1
3D 1H-15N NOESY	15N	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
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 H(CCO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - processing

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure solution

CARA v1.8.4.2, Keller and Wuthrich - chemical shift assignment

TALOS+, Cornilescu, Delaglio and Bax - structure solution

ATNOS, Herrmann, Guntert and Wuthrich - peak picking

CANDID, Herrmann, Guntert and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 600 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz
Bruker Avance 950 MHz

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