3R7C | pdb_00003r7c

The structure of a hexahestidine-tagged form of augmenter of liver regeneration reveals a novel Cd(2)Cl(4)O(6) cluster that aids in crystal packing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.211 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The structure of augmenter of liver regeneration crystallized in the presence of 50 mM CdCl2 reveals a novel Cd2Cl4O6 cluster that aids in crystal packing.

Florence, Q.Wu, C.K.Habel, J.Swindell 2nd, J.T.Wang, B.C.Rose, J.P.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1128-1133

  • DOI: https://doi.org/10.1107/S0907444912022561
  • Primary Citation of Related Structures:  
    3R7C

  • PubMed Abstract: 

    The crystal structure of the protein augmenter of liver regeneration containing a 14-residue hexahistidine purification tag (hsALR) has been determined to 2.4 Å resolution by Cd-SAD using a highly redundant data set collected on a rotating-anode home X-ray source and processed in 1998. The hsALR crystal structure is a tetramer composed of two homodimers bridged by a novel Cd(2)Cl(4)O(6) cluster via binding to the side-chain carboxylate groups of two solvent-exposed aspartic acid residues. A comparison with the native sALR tetramer shows that the cluster dramatically changes the hsALR dimer-dimer interface, which can now better accommodate the extra 14 N-terminal residues associated with the purification tag. The refined 2.4 Å resolution structure is in good agreement with both the X-ray data (R(cryst) of 0.165, R(free) of 0.211) and the expected stereochemistry (r.m.s. deviations from ideality for bond lengths and bond angles of 0.007 Å and 1.15°, respectively).


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-linked sulfhydryl oxidase ALR
A, B, C, D
139Rattus norvegicusMutation(s): 0 
Gene Names: AlrGferGfer (ALR)
EC: 1.8.3.2
UniProt
Find proteins for Q63042 (Rattus norvegicus)
Explore Q63042 
Go to UniProtKB:  Q63042
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63042
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
S [auth C],
V [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B],
P [auth B],
T [auth C]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
W [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth A]
K [auth A]
L [auth A]
F [auth A],
G [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
U [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.211 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.688α = 90
b = 99.688β = 90
c = 113.61γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2025-11-12
    Changes: Database references