1NE8

YDCE protein from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of YdcE protein from Bacillus subtilis

Gogos, A.Mu, H.Bahna, F.Gomez, C.A.Shapiro, L.

(2003) PROTEINS: STRUCT.,FUNCT.,GENET. 53: 320-322


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
conserved hypothetical protein YDCE
A
117Bacillus subtilis (strain 168)Gene Names: ndoA (mazF, ydcE)
EC: 3.1.27.-
Find proteins for P96622 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P96622
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download SDF File 
Download CCD File 
A
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.159 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.630α = 90.00
b = 56.630β = 90.00
c = 138.257γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
RESOLVEphasing
SOLVEphasing
REFMACrefinement
SCALEPACKdata scaling
RESOLVEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description