2P0I

Crystal structure of L-rhamnonate dehydratase from Gibberella zeae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of L-Rhamnonate Dehydratase from Gibberella Zeae

Patskovsky, Y.Toro, R.Sauder, J.M.Dickey, M.Logan, C.Gheyi, T.Wasserman, S.R.Smith, D.Gerlt, J.Burley, S.K.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-rhamnonate dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H
456Fusarium graminearumMutation(s): 6 
Gene Names: FG09883.1
EC: 4.2.1.90
UniProt
Find proteins for D0VX14 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1))
Explore D0VX14 
Go to UniProtKB:  D0VX14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VX14
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
I [auth A]
KA [auth H]
LA [auth H]
N [auth B]
AA [auth F],
I [auth A],
KA [auth H],
LA [auth H],
N [auth B],
O [auth B],
Q [auth C],
R [auth D],
S [auth D],
V [auth E],
W [auth E],
X [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
DA [auth F]
EA [auth F]
FA [auth G]
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth F],
FA [auth G],
GA [auth G],
HA [auth G],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
L [auth A],
M [auth A],
MA [auth H],
NA [auth H],
P [auth B],
T [auth D],
U [auth D],
Y [auth E],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
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: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.404α = 90
b = 201.135β = 90
c = 82.402γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2018-11-14
    Changes: Data collection, Structure summary
  • Version 1.5: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary