NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.

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NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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04-27-2011, 04:03 PM

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NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.

NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.

NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554.

Protein Sci. 2011 Apr 21;

Authors: Atia-Tul-Wahab , Serrano P, Geralt M, Wüthrich K

The solution structure of the hypothetical phage-related protein NP_888769.1 from the gram-negative bacterium Bordetella bronchoseptica contains a well-structured core comprising a five-stranded, antiparallel ?-sheet packed on one side against two ?-helices and a short ?-hairpin with three flexibly disordered loops extending from the central ?-sheet. A homology search with the software DALI identified two Protein Data Bank deposits with Z-scores > 8, where both of these proteins have less than 8% sequence identity relative to NP_888769.1, and one has been functionally annotated as a lambda phage tail terminator protein. A sequence-homology analysis then confirmed that NP_888769.1 represents the first three-dimensional structural representative of a new protein family that was previously predicted by the Joint Center for Structural Genomics, which includes so far about twenty prophage proteins encoded in bacterial genomes.

PMID: 21520320 [PubMed - as supplied by publisher]

Source: PubMed

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