BMRB Entry 15373

Name: The prokaryotic Cys2His2 zinc finger adopts a novel fold as revealed by the NMR structure of A. tumefaciens Ros DNA binding domain
Published: 2008-03-13

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PDB ID: 2jsp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15373
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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:

The prokaryotic Cys2His2 zinc finger adopts a novel fold as revealed by the NMR structure of A. tumefaciens Ros DNA binding domain

Deposition date:

2007-07-10

Original release date:

2008-03-13

Authors:

Malgieri, Gaetano

Citation:

Citation: Malgieri, Gaetano; Russo, L.; Esposito, S.; Baglivo, I.; Zaccaro, L.; Pedone, E.; Di Blasio, B.; Isernia, C.; Pedone, P.; Fattorusso, R.. "The prokaryotic Cys2His2 zinc finger adopts a novel fold as revealed by the NMR structure of A.tumefaciens Ros DNA binding domain" Proc. Natl. Acad. Sci. U.S.A. 104, 17341-17346 (2007).
PubMed: 17956987

Assembly members:

Assembly members:
Ros87_polypeptide, polymer, 87 residues, 9959.560 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Agrobacterium tumefaciens Taxonomy ID: 358 Superkingdom: Bacteria Kingdom: not available Genus/species: Agrobacterium tumefaciens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-11d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ros87_polypeptide: AVNVEKQKPAVSVRKSVQDD HIVCLECGGSFKSLKRHLTT HHSMTPEEYREKWDLPVDYP MVAPAYAEARSRLAKEMGLG QRRKANR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	341
15N chemical shifts	85
1H chemical shifts	505

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ros87 polypeptide	1
2	ZINC ION	2

Entities:

Entity 1, Ros87 polypeptide 87 residues - 9959.560 Da.

1

ALA

VAL

ASN

VAL

GLU

LYS

GLN

LYS

PRO

ALA

2

VAL

SER

VAL

ARG

LYS

SER

VAL

GLN

ASP

3

HIS

ILE

VAL

CYS

LEU

GLU

CYS

GLY

SER

4

PHE

LYS

SER

LEU

LYS

ARG

HIS

LEU

THR

5

HIS

SER

MET

THR

PRO

GLU

TYR

ARG

6

GLU

LYS

TRP

ASP

LEU

PRO

VAL

ASP

TYR

PRO

7

MET

VAL

ALA

PRO

ALA

TYR

ALA

GLU

ALA

ARG

8

SER

ARG

LEU

ALA

LYS

GLU

MET

GLY

LEU

GLY

9

GLN

ARG

LYS

ALA

ASN

ARG

Entity 2, ZINC ION - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Ros87, [U-100% 15N], 1 mM; Zinc ion 1 mM; phosphate buffer 20 mM; NaCl 0.2 M

sample_2: Ros87, [U-100% 13C; U-100% 15N], 1 mM; Zinc ion 1 mM; phosphate buffer 20 mM; NaCl 0.2 M

sample_3: Ros87 1 mM; Zinc ion 1 mM; phosphate buffer 20 mM; NaCl 0.2 M

sample_conditions_1: ionic strength: 0.2 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D CBCANH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC IPAP	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC IPAP	sample_2	anisotropic	sample_conditions_1

Software:

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

ProcheckNMR, Laskowski and MacArthur - structure validation

VNMRJ, Varian - collection, processing

ModelFree, Palmer - Calculation dynamic parameters, data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis, figure realization, structure visualization

SPDB, Guex, N. and Peitsch, M. C. - Energy minimization

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Bruker Avance 500 MHz
Bruker Avance 800 MHz

PDB	2JSP
EMBL	CAA58116 CDI07817 CDN91482
GB	AAA22106 AAK86720 ADY63837 AHK00781 AKC06614
REF	NP_353935 WP_003497181 WP_003509257 WP_003512037 WP_004440665
SP	P55324 Q04152
AlphaFold	P55324 Q04152