5NQD | pdb_00005nqd

Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A

PDB DOI: https://doi.org/10.2210/pdb5NQD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudorhizobium banfieldiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-20 Released: 2018-05-30
Deposition Author(s): Santos-Silva, T., Romao, M., Vieira, M., Marques, A.T.
Funding Organization(s): FCT, PT2020

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.172 (Depositor), 0.179 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A

Santos-Silva, T., Romao, M., Vieira, M., Marques, A.T.

To be published.

Macromolecule Content

Total Structure Weight: 439.75 kDa
Atom Count: 32,195
Modeled Residue Count: 3,900
Deposited Residue Count: 3,900
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AroA	A, C, E, G	843	Pseudorhizobium banfieldiae	Mutation(s): 0 Gene Names: aroA, aioA, NT26_p10030 EC: 1.20.98.1
UniProt
Find proteins for Q6VAL8 (Pseudorhizobium banfieldiae) Explore Q6VAL8 Go to UniProtKB: Q6VAL8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6VAL8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster	B, D, F, H	132	Pseudorhizobium banfieldiae	Mutation(s): 0 Gene Names: aioB, NT26_p10029 EC: 1.20.98.1
UniProt
Find proteins for L0NMC5 (Pseudorhizobium banfieldiae) Explore L0NMC5 Go to UniProtKB: L0NMC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L0NMC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain RA [auth G] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain SA [auth G] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain RA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain RA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain J [auth A]	I [auth A] IA [auth E] J [auth A] JA [auth E] RA [auth G] I [auth A], IA [auth E], J [auth A], JA [auth E], RA [auth G], SA [auth G], V [auth C], W [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 I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain V [auth C] Focus chain W [auth C]
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain YA [auth G] MOL2 format, chain ZA [auth G] MOL2 format, chain YA [auth G] mmCIF format, chain ZA [auth G] mmCIF format, chain YA [auth G]	YA [auth G], ZA [auth G]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain YA [auth G] Focus chain ZA [auth G]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain VA [auth G] SDF format, chain Z [auth C] SDF format, chain MA [auth E] SDF format, chain M [auth A] MOL2 format, chain VA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth A] mmCIF format, chain VA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth A]	M [auth A], MA [auth E], VA [auth G], Z [auth C]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain MA [auth E] Focus chain VA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain M [auth A] Focus chain MA [auth E] Focus chain VA [auth G] Focus chain Z [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain HA [auth D] SDF format, chain QA [auth F] SDF format, chain T [auth B] MOL2 format, chain DB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain QA [auth F] MOL2 format, chain T [auth B] mmCIF format, chain DB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain QA [auth F] mmCIF format, chain T [auth B]	DB [auth H], HA [auth D], QA [auth F], T [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DB [auth H] Focus chain HA [auth D] Focus chain QA [auth F] Focus chain T [auth B] Interactions & Density Focus chain DB [auth H] Focus chain HA [auth D] Focus chain QA [auth F] Focus chain T [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain EA [auth C]	EA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Interactions & Density Focus chain EA [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain NA [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain N [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain NA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain N [auth A]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] N [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], N [auth A], NA [auth E], O [auth A], OA [auth E], P [auth A], Q [auth A], WA [auth G], XA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain WA [auth G] Focus chain XA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain WA [auth G] Focus chain XA [auth G]
4MO Query on 4MO Download:Ideal Coordinates CCD File SDF format, chain LA [auth E] SDF format, chain Y [auth C] SDF format, chain UA [auth G] SDF format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain Y [auth C] MOL2 format, chain UA [auth G] MOL2 format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain Y [auth C] mmCIF format, chain UA [auth G] mmCIF format, chain L [auth A]	L [auth A], LA [auth E], UA [auth G], Y [auth C]	MOLYBDENUM(IV) ION Mo ZIKKVZAYJJZBGE-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain LA [auth E] Focus chain UA [auth G] Focus chain Y [auth C] Interactions & Density Focus chain L [auth A] Focus chain LA [auth E] Focus chain UA [auth G] Focus chain Y [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain FA [auth C] SDF format, chain S [auth A] SDF format, chain PA [auth E] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain PA [auth E] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain FA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain PA [auth E]	AB [auth G], BB [auth G], FA [auth C], PA [auth E], S [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth C] Focus chain PA [auth E] Focus chain S [auth A] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth C] Focus chain PA [auth E] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain GA [auth C] SDF format, chain U [auth B] MOL2 format, chain CB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain U [auth B] mmCIF format, chain CB [auth G] mmCIF format, chain GA [auth C] mmCIF format, chain U [auth B]	CB [auth G], GA [auth C], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain GA [auth C] Focus chain U [auth B] Interactions & Density Focus chain CB [auth G] Focus chain GA [auth C] Focus chain U [auth B]
O Query on O Download:Ideal Coordinates CCD File SDF format, chain KA [auth E] SDF format, chain X [auth C] SDF format, chain TA [auth G] SDF format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain X [auth C] MOL2 format, chain TA [auth G] MOL2 format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain X [auth C] mmCIF format, chain TA [auth G] mmCIF format, chain K [auth A]	K [auth A], KA [auth E], TA [auth G], X [auth C]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain KA [auth E] Focus chain TA [auth G] Focus chain X [auth C] Interactions & Density Focus chain K [auth A] Focus chain KA [auth E] Focus chain TA [auth G] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.172 (Depositor), 0.179 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.408	α = 90
b = 148.665	β = 90
c = 232.009	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Funding Organization	Location	Grant Number
FCT	Portugal	PTDC/BBB-BEP/1185/2014
FCT	Portugal	UID/Multi/04378/2013
FCT	Portugal	PTDC/QEQ-MED/1902/2014
PT2020	Portugal	POCI-01-0145-FEDER-007728

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 2.0: 2018-10-03
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary