3FDJ

The structure of a DegV family protein from Eubacterium eligens.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a DegV family protein from Eubacterium eligens.

Cuff, M.E.Hendricks, R.Freeman, L.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DegV family protein
A
278[Eubacterium] eligensMutation(s): 0 
Find proteins for D0VX07 ([Eubacterium] eligens)
Go to UniProtKB:  D0VX07
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.445α = 90.00
b = 57.445β = 90.00
c = 186.558γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
DENZOdata reduction
PDB_EXTRACTdata extraction
DMphasing
MLPHAREphasing
SCALEPACKdata scaling
SHELXDphasing
CCP4phasing
Omodel building
REFMACrefinement
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
HKL-3000phasing
SBC-Collectdata collection
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description