1G8K

CRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES FAECALIS

PDB DOI: https://doi.org/10.2210/pdb1G8K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Alcaligenes faecalis
Mutation(s): No

Deposited: 2000-11-17 Released: 2000-12-13
Deposition Author(s): Ellis, P.J., Conrads, T., Hille, R., Kuhn, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.179
R-Value Work: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 11250197 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(01)00566-4
Primary Citation of 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.

Organizational Affiliation

Stanford Synchrotron Radiation Laboratory, Stanford University, 94309, Stanford, CA, USA.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARSENITE OXIDASE	A, C, E, G	825	Alcaligenes faecalis	Mutation(s): 0
UniProt
Find proteins for Q7SIF4 (Alcaligenes faecalis) Explore Q7SIF4 Go to UniProtKB: Q7SIF4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SIF4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARSENITE OXIDASE	B, D, F, H	133	Alcaligenes faecalis	Mutation(s): 0
UniProt
Find proteins for Q7SIF3 (Alcaligenes faecalis) Explore Q7SIF3 Go to UniProtKB: Q7SIF3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SIF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain Z [auth C] SDF format, chain MA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain MA [auth E]	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		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BB [auth G] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BB [auth G] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain Z [auth C]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EB [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E]	DA [auth C], EB [auth G], Q [auth A], QA [auth E]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain EB [auth G] Focus chain Q [auth A] Focus chain QA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EB [auth G] Focus chain Q [auth A] Focus chain QA [auth E]
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HB [auth H] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain T [auth B] SDF format, chain UA [auth F] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain XA [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G]	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		Interactions Focus chain GA [auth D] Focus chain HB [auth H] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain T [auth B] Focus chain UA [auth F] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Interactions & Density Focus chain GA [auth D] Focus chain HB [auth H] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain T [auth B] Focus chain UA [auth F] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain IB [auth H] SDF format, chain U [auth B] SDF format, chain VA [auth F] MOL2 format, chain HA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth F]	HA [auth D], IB [auth H], U [auth B], VA [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain IB [auth H] Focus chain U [auth B] Focus chain VA [auth F] Interactions & Density Focus chain HA [auth D] Focus chain IB [auth H] Focus chain U [auth B] Focus chain VA [auth F]
4MO Query on 4MO Download Ideal Coordinates CCD File SDF format, chain DB [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain CA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain CA [auth C]	CA [auth C], DB [auth G], P [auth A], PA [auth E]	MOLYBDENUM(IV) ION Mo ZIKKVZAYJJZBGE-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DB [auth G] Focus chain P [auth A] Focus chain PA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain DB [auth G] Focus chain P [auth A] Focus chain PA [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GB [auth G] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain TA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GB [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E]	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		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GB [auth G] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain TA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GB [auth G] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain TA [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G]	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		Interactions Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G]
O Query on O Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CB [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E]	BA [auth C], CB [auth G], O [auth A], OA [auth E]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth G] Focus chain O [auth A] Focus chain OA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth G] Focus chain O [auth A] Focus chain OA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.179
R-Value Work: 0.154
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.74	α = 97.71
b = 109.52	β = 90
c = 117.64	γ = 96.43

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
CNS	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-12-13

Deposition Author(s):

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