2I6E | pdb_00002i6e

Crystal structure of protein DR0370 from Deinococcus radiodurans, Pfam DUF178

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.235 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2I6E

This is version 1.4 of the entry. See complete history. 

Literature

X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family.

Tyagi, R., Burley, S.K., Swaminathan, S.

(2007) BMC Struct Biol 7: 62-62

  • DOI: https://doi.org/10.1186/1472-6807-7-62
  • Primary Citation Related Structures: 
    2I6E

  • PubMed Abstract: 

    Pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. Pfam has two large series of functionally uncharacterized families, known as Domains of Unknown Function (DUFs) and Uncharacterized Protein Families (UPFs). Crystal structures of two proteins from Deinococcus radiodurans and Streptomyces coelicolor belonging to Pfam protein family DUF178 (ID: PF02621) have been determined using Selenium-Single-wavelength Anomalous Dispersion (Se-SAD). Based on the structure, we have identified the putative function for this family of protein. Unexpectedly, we found that DUF178 Pfam is remarkably similar to Pfam family DUF191 suggesting that the sequence-based classification alone may not be sufficient to classify proteins into Pfam families.

    • Organizational Affiliation: 
    • Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA. swami@bnl.gov

Macromolecule Content 

  • Total Structure Weight: 268.64 kDa 
  • Atom Count: 17,623 
  • Modeled Residue Count: 2,176 
  • Deposited Residue Count: 2,408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein
A, B, C, D, E
A, B, C, D, E, F, G, H
301Deinococcus radioduransMutation(s): 4 
Gene Names: DR_0370
EC: 4.2.1.151
UniProt
Find proteins for Q9RXE3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RXE3 
Go to UniProtKB:  Q9RXE3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RXE3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4


Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth E],
S [auth E],
T [auth F],
U [auth F],
V [auth F],
W [auth G],
X [auth G],
Y [auth G],
Z [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.235 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.31α = 90
b = 139.37β = 92.79
c = 153.615γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2007-10-11
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Structure summary