BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 15373

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PDB ID:
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
MolProbity Validation Chart

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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   PubMed: 17956987

Deposition date: 2007-07-10 Original release date: 2008-03-13

Authors: Malgieri, Gaetano

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).

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts341
15N chemical shifts85
1H chemical shifts505

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ros87 polypeptide1
2ZINC ION2

Entities:

Entity 1, Ros87 polypeptide 87 residues - 9959.560 Da.

1   ALAVALASNVALGLULYSGLNLYSPROALA
2   VALSERVALARGLYSSERVALGLNASPASP
3   HISILEVALCYSLEUGLUCYSGLYGLYSER
4   PHELYSSERLEULYSARGHISLEUTHRTHR
5   HISHISSERMETTHRPROGLUGLUTYRARG
6   GLULYSTRPASPLEUPROVALASPTYRPRO
7   METVALALAPROALATYRALAGLUALAARG
8   SERARGLEUALALYSGLUMETGLYLEUGLY
9   GLNARGARGLYSALAASNARG

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D CBCANHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_2isotropicsample_conditions_1
2D 1H-15N HSQC IPAPsample_2anisotropicsample_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

Related Database Links:

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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts