8YEB | pdb_00008yeb

Crystal structure of L-ribulose 3-epimerase from Arthrobacter globiformis M30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of L-ribulose 3-epimerase from Arthrobacter globiformis M30

Watanabe, M.Nakamich, Y.Mine, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketose 3-epimerase297Arthrobacter globiformisMutation(s): 0 
Gene Names: DAE
EC: 5.1.3
UniProt
Find proteins for A0A1L7NQ96 (Arthrobacter globiformis)
Explore A0A1L7NQ96 
Go to UniProtKB:  A0A1L7NQ96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L7NQ96
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth G],
S [auth E],
V [auth C],
Y [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth H]
CA [auth I]
DA [auth J]
EA [auth K]
FA [auth L]
BA [auth H],
CA [auth I],
DA [auth J],
EA [auth K],
FA [auth L],
GA [auth M],
HA [auth N],
IA [auth O],
JA [auth P],
Q [auth A],
R [auth E],
T [auth B],
U [auth C],
W [auth D],
X [auth F],
Z [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.095α = 90
b = 148.264β = 94.97
c = 136.707γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release