3VEX

Crystal structure of the O-carbamoyltransferase TobZ H14N variant in complex with carbamoyl adenylate intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.

Parthier, C.Gorlich, S.Jaenecke, F.Breithaupt, C.Brauer, U.Fandrich, U.Clausnitzer, D.Wehmeier, U.F.Bottcher, C.Scheel, D.Stubbs, M.T.

(2012) Angew Chem Int Ed Engl 51: 4046-4052


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-carbamoyltransferase TobZ576Streptoalloteichus tenebrariusMutation(s): 1 
Gene Names: tacAtobZ
EC: 2.1.3
UniProt
Find proteins for Q70IY1 (Streptoalloteichus tenebrarius (strain ATCC 17920 / DSM 40477 / JCM 4838 / CBS 697.72 / NBRC 16175 / NCIMB 11028 / NRRL B-12390 / A12253. 1))
Explore Q70IY1 
Go to UniProtKB:  Q70IY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70IY1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA0
Query on CA0

Download Ideal Coordinates CCD File 
C [auth A]5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine
C11 H15 N6 O8 P
CHSNPOFVFYPELH-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.648α = 90
b = 98.648β = 90
c = 280.229γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Database references
  • Version 1.2: 2012-05-02
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description