3BYW

Crystal structure of an extracellular domain of arabinofuranosyltransferase from Corynebacterium diphtheriae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of an extracellular domain of arabinofuranosyltransferase from Corynebacterium diphtheriae.

Tan, K.Hatzos, C.Abdullah, J.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative arabinofuranosyltransferase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
177Corynebacterium diphtheriae NCTC 13129Mutation(s): 0 
Gene Names: DIP0159
UniProt
Find proteins for Q6NK78 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore Q6NK78 
Go to UniProtKB:  Q6NK78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NK78
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
I [auth A],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
I [auth A],
IA [auth F],
J [auth A],
JA [auth F],
KA [auth G],
L [auth B],
LA [auth G],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth D],
FA [auth E],
GA [auth E],
HA [auth E],
K [auth A],
AA [auth D],
FA [auth E],
GA [auth E],
HA [auth E],
K [auth A],
MA [auth G],
NA [auth H],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
Y [auth D],
Z [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
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: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.885α = 90
b = 80.619β = 110.91
c = 115.826γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance