3VO0

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum covalent-bonded with 2-deoxy-2-fluoro-D-glucuronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-Glucuronidase488Acidobacterium capsulatum ATCC 51196Mutation(s): 0 
Gene Names: ACP_2665
EC: 3.2.1.31
UniProt
Find proteins for C1F2K5 (Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161))
Explore C1F2K5 
Go to UniProtKB:  C1F2K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1F2K5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GUF
Query on GUF

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A]
2-deoxy-2-fluoro-beta-D-glucopyranuronic acid
C6 H9 F O6
LDVYRSUUUDDWHG-LVBGKUAWSA-N
GUZ
Query on GUZ

Download Ideal Coordinates CCD File 
B [auth A]2-deoxy-2-fluoro-alpha-D-glucopyranuronic acid
C6 H9 F O6
LDVYRSUUUDDWHG-CLQWQSTFSA-N
DNF
Query on DNF

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A]
2,4-DINITROPHENOL
C6 H4 N2 O5
UFBJCMHMOXMLKC-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.489α = 90
b = 101.489β = 90
c = 218.238γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary