1G8K | pdb_00001g8k

CRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES FAECALIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.179 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.149 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.

Ellis, P.J.Conrads, T.Hille, R.Kuhn, P.

(2001) Structure 9: 125-132

  • DOI: https://doi.org/10.1016/s0969-2126(01)00566-4
  • Primary Citation Related Structures: 
    1G8J, 1G8K

  • PubMed Abstract: 

    Arsenite oxidase from Alcaligenes faecalis NCIB 8687 is a molybdenum/iron protein involved in the detoxification of arsenic. It is induced by the presence of AsO(2-) (arsenite) and functions to oxidize As(III)O(2-), which binds to essential sulfhydryl groups of proteins and dithiols, to the relatively less toxic As(V)O(4)(3-) (arsenate) prior to methylation. Using a combination of multiple isomorphous replacement with anomalous scattering (MIRAS) and multiple-wavelength anomalous dispersion (MAD) methods, the crystal structure of arsenite oxidase was determined to 2.03 A in a P2(1) crystal form with two molecules in the asymmetric unit and to 1.64 A in a P1 crystal form with four molecules in the asymmetric unit. Arsenite oxidase consists of a large subunit of 825 residues and a small subunit of approximately 134 residues. The large subunit contains a Mo site, consisting of a Mo atom bound to two pterin cofactors, and a [3Fe-4S] cluster. The small subunit contains a Rieske-type [2Fe-2S] site. The large subunit of arsenite oxidase is similar to other members of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes, particularly the dissimilatory periplasmic nitrate reductase from Desulfovibrio desulfuricans, but is unique in having no covalent bond between the polypeptide and the Mo atom. The small subunit has no counterpart among known Mo protein structures but is homologous to the Rieske [2Fe-2S] protein domain of the cytochrome bc(1) and cytochrome b(6)f complexes and to the Rieske domain of naphthalene 1,2-dioxygenase.


  • Organizational Affiliation
    • Stanford Synchrotron Radiation Laboratory, Stanford University, 94309, Stanford, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 435.21 kDa 
  • Atom Count: 34,251 
  • Modeled Residue Count: 3,820 
  • Deposited Residue Count: 3,832 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ARSENITE OXIDASE
A, C, E, G
825Alcaligenes faecalisMutation(s): 0 
EC: 1.20.9.1
UniProt
Find proteins for Q7SIF4 (Alcaligenes faecalis)
Explore Q7SIF4 
Go to UniProtKB:  Q7SIF4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ARSENITE OXIDASE
B, D, F, H
133Alcaligenes faecalisMutation(s): 0 
EC: 1.20.9.1
UniProt
Find proteins for Q7SIF3 (Alcaligenes faecalis)
Explore Q7SIF3 
Go to UniProtKB:  Q7SIF3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD

Query on MGD



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth G]
BB [auth G]
M [auth A]
MA [auth E]
AA [auth C],
AB [auth G],
BB [auth G],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
Z [auth C]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
DA [auth C],
EB [auth G],
Q [auth A],
QA [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
HG

Query on HG



Download:Ideal Coordinates CCD File
GA [auth D]
HB [auth H]
I [auth A]
IA [auth E]
J [auth A]
GA [auth D],
HB [auth H],
I [auth A],
IA [auth E],
J [auth A],
JA [auth E],
T [auth B],
UA [auth F],
V [auth C],
W [auth C],
WA [auth G],
XA [auth G]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
HA [auth D],
IB [auth H],
U [auth B],
VA [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
4MO

Query on 4MO



Download:Ideal Coordinates CCD File
CA [auth C],
DB [auth G],
P [auth A],
PA [auth E]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
EA [auth C]
FA [auth C]
FB [auth G]
GB [auth G]
R [auth A]
EA [auth C],
FA [auth C],
FB [auth G],
GB [auth G],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
TA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A]
KA [auth E]
L [auth A]
LA [auth E]
X [auth C]
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
X [auth C],
Y [auth C],
YA [auth G],
ZA [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
O

Query on O



Download:Ideal Coordinates CCD File
BA [auth C],
CB [auth G],
O [auth A],
OA [auth E]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.179 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.149 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.74α = 97.71
b = 109.52β = 90
c = 117.64γ = 96.43
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-10-05
    Changes: Other
  • Version 1.4: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary