3H0N

Crystal structure of a duf1470 family protein (jann_2411) from jannaschia sp. ccs1 at 1.45 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45  resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator.

Bakolitsa, C.Bateman, A.Jin, K.K.McMullan, D.Krishna, S.S.Miller, M.D.Abdubek, P.Acosta, C.Astakhova, T.Axelrod, H.L.Burra, P.Carlton, D.Chiu, H.J.Clayton, T.Das, D.Deller, M.C.Duan, L.Elias, Y.Feuerhelm, J.Grant, J.C.Grzechnik, A.Grzechnik, S.K.Han, G.W.Jaroszewski, L.Klock, H.E.Knuth, M.W.Kozbial, P.Kumar, A.Marciano, D.Morse, A.T.Murphy, K.D.Nigoghossian, E.Okach, L.Oommachen, S.Paulsen, J.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.Trame, C.B.Trout, C.V.van den Bedem, H.Weekes, D.White, A.Xu, Q.Hodgson, K.O.Wooley, J.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.Wilson, I.A.

(2010) Acta Crystallogr.,Sect.F 66: 1198-1204

  • DOI: 10.1107/S1744309109025196

  • PubMed Abstract: 
  • The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This ...

    The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.


    Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
uncharacterized protein DUF1470
A
188Jannaschia sp. (strain CCS1)N/A
Find proteins for Q28PN4 (Jannaschia sp. (strain CCS1))
Go to UniProtKB:  Q28PN4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 77.750α = 90.00
b = 59.670β = 128.79
c = 57.820γ = 90.00
Software Package:
Software NamePurpose
MolProbitymodel building
SOLVEphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description