PubMed ID is not available.
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Filling out the structural map of the NTF2-like superfamily.
(2013) BMC Bioinformatics 14
PubMed: 24246060 | PubMedCentral: PMC3924330 | DOI: 10.1186/1471-2105-14-327
jejuni serotype O:2 (strain NCTC 11168) [PDB:3K7C], rumgna_01855) and RUMGNA_01855 from Ruminococcus gnavus (strain ATCC 29149) [PDB:4HYZ] have been solved by X-ray crystallography.
Comparison of these three structures showed that they are significantly similar to each other, especially for [PDB:3K7C] and [PDB:4HYZ].
Data collection and refinement statistics (PDB 4hyz).
The structure of [PDB:3K7C] differs from that of [PDB:3KZT] and [PDB:4HYZ] in that it lacks the edge strands in the beta-sheet but has a longer helix on the opposite side.
[PDB:4HYZ] is a member of DUF3887, [PDB:3K7C] is a member of DUF4878 and [PDB:3KZT] is a member of DUF3828.
X-ray diffraction data were collected from a single crystal at wavelengths corresponding to the inflection (λ 1 ), high energy remote (λ 2 ), and peak (λ 3 ) [PDB:3K7C]; the peak(λ 1 ), inflection (λ 2 ), and high energy remote (λ 3 ) [PDB: 4HYZ]; or the inflection (λ 1 ) and high energy remote (λ 2 ) [PDB:3KZT], of a multi-wavelength or a two-wavelength selenium multi-wavelength anomalous diffraction (MAD).
It is significantly less similar to [PDB:3K7C] (maximum Z-score of 6.4 when compared to chain A), and [PDB:4HYZ] (maximum Z-score of 6.8 when compared to chain B).
Model completion was performed using the interactive computer-graphics program COOT [ 42 ] and MAD-phase-restrained refinement was accomplished using the program REFMAC ver 5.5.0102 [PDB:3K7C], ver 5.5.0053 [PDB:3KZT] [ 43 ] or BUSTER ver 2.10.0 [ 44 ] [PDB:4HYZ].
Here we describe the first crystal structures of three Pfam families with NTF2-like folds: DUF3828 [PDB:3KZT] [Pfam:PF12883], DUF3887 [PDB:4HYZ] [Pfam:PF13026] and DUF4878 [PDB:3K7C] [Pfam:PF12870].
FATCAT results showed that the structures of [PDB:3KZT] and [PDB:4HYZ] are significantly similar with P-value of 1.53e- 03 and the structure alignment has 85 equivalent positions with an RMSD of 1.72 Å; the structures of [PDB:3KZT] and [PDB:3K7C] are significantly similar with P-value of 2.57e- 03 and the structure alignment has 95 equivalent positions with an RMSD of 2.53 Å; the structures of [PDB:4HYZ] and [PDB:3K7C] are significantly similar with P-value of 1.55e- 06 and the structure alignment has 95 equivalent positions with an RMSD of 2.99 Å [ 19 ].
[PDB:4HYZ] has a cavity of a similar size in a similar position with weakly positive electrostatic potential.
The data were integrated and scaled using the XDS and XSCALE programs respectively [ 32 , 33 ] [PDB:3K7C] or the MOSFLM [ 34 ] and SCALA [ 35 ] programs [PDB:3KZT][PDB:4HYZ].
Sequence conservation in the region of the cavities in [PDB:3K7C] and in [PDB:4HYZ] is poor.
Table 1 Percentage identity of the three proteins for which structure has been determined, calculated using DALI [ 24 ] PDB ID 3KZT 3K7C 4HYZ 3KZT 11% 14% 3K7C 11% 10% 4HYZ 14% 10% DALI [ 24 ] searches revealed that [PDB:3KZC] and [PDB:4HYZ] are more similar to each other than they are to most other members of the NTF2-like superfamily (Z-score 9.8), however [PDB:3KZT] is more distantly related.
Atomic coordinates and experimental structure factors have been deposited in the PDB and are accessible under the codes [PDB:3KZT], [PDB:3K7C] and [PDB:4HYZ].
The crystal structure of a DUF3887 protein, the hypothetical protein Rumgna_01855 [UniProtKB:A7B2S7] from Ruminococcus gnavus (strain ATCC 29149), was determined to 2.25 Å resolution by MAD method and was deposited to PDB as [PDB:4HYZ].
The three structures ([PDB:3K7C], [PDB:3KZT] and [PDB:4HYZ]) all possess NTF2-like folds, despite being dissimilar in sequence (Figures 6 and 7 , Table 1 ).
[PDB:4HYZ] and [PDB:3K7C] are most similar to members of the SnoAL_3 family [Pfam:PF13474] including [PDB:3GWR] (Z-score 10.1 when compared to [PDB:3K7C]), and the SnoAL_2 family [Pfam:PF12860] including [PDB:3D9R] (Z-score 9.5 when compared to [PDB:3K7C]).
Iterative automated model building was performed with RESOLVE [ 38 ] at a resolution of 2.00 Å [PDB:3K7C] or Arp/Warp [ 39 ] at a resolution of 2.15 Å [PDB:3KZT] or with Buccaneer [ 40 , 41 ] at a resolution of 2.25 Å [PDB:4HYZ] from density-modified electron density.
Publication Year: 2013
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.