6NHU

Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of the Beta Lactamase Class D YbxI from Agrobacterium fabrum

Kim, Y.Welk, L.Endres, M.Babnigg, G.Joachimiak, A.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C, D
252Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
EC: 3.5.2.6
Find proteins for Q7D0B8 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q7D0B8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.879α = 90.00
b = 165.957β = 90.02
c = 75.428γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
MOLREPphasing
HKL-3000phasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States--

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release