3GYR | pdb_00003gyr

Structure of Phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center.

PDB DOI: https://doi.org/10.2210/pdb3GYR/pdb
Entry: 3GYR supersedes: 2G23

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces antibioticus
Expression System: Streptomyces lividans
Mutation(s): Yes

Deposited: 2009-04-05 Released: 2009-04-28
Deposition Author(s): Smith, A.W., Camara-Artigas, A., Wang, M., Francisco, W.A., Allen, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of Phenoxazinone Synthase from Streptomyces Antibioticus Reveals a New Type 2 Copper Center.

Smith, A.W., Camara-Artigas, A., Wang, M., Allen, J.P., Francisco, W.A.

(2006) Biochemistry 45: 4378

PubMed: 16584173 Search on PubMed
DOI: https://doi.org/10.1021/bi0525526
Primary Citation Related Structures:
3GYR

PubMed Abstract:
The multicopper oxidase phenoxazinone synthase (PHS) catalyzes the penultimate step in the biosynthesis of the antibiotic actinomycin D by Streptomyces antibioticus. PHS exists in two oligomeric forms: a dimeric form and a hexameric form, with older actinomycin-producing cultures containing predominately the hexameric form. The structure of hexameric PHS has been determined using X-ray diffraction to a resolution limit of 2.30 A and is found to contain several unexpected and distinctive features. The structure forms a hexameric ring that is centered on a pseudo 6-fold axis and has an outer diameter of 185 A with a large central cavity that has a diameter of 50 A. This hexameric structure is stabilized by a long loop connecting two domains; bound to this long loop is a fifth copper atom that is present as a type 2 copper. This copper atom is not present in any other multicopper oxidase, and its presence appears to stabilize the hexameric structure.

Organizational Affiliation

Department of Chemistry and Biochemistry, Arizona State University, Tempe Arizona 85287-1604, USA.

Macromolecule Content

Total Structure Weight: 810.24 kDa
Atom Count: 59,241
Modeled Residue Count: 7,044
Deposited Residue Count: 7,344
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenoxazinone synthase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	612	Streptomyces antibioticus	Mutation(s): 1 Gene Names: phsA EC: 1 (PDB Primary Data), 1.10.3.4 (UniProt)
UniProt
Find proteins for Q53692 (Streptomyces antibioticus) Explore Q53692 Go to UniProtKB: Q53692
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2O Query on C2O Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain YA [auth H] SDF format, chain U [auth B] SDF format, chain TA [auth G] SDF format, chain SB [auth L] SDF format, chain P [auth A] SDF format, chain OA [auth F] SDF format, chain NB [auth K] SDF format, chain JA [auth E] SDF format, chain IB [auth J] SDF format, chain EA [auth D] SDF format, chain DB [auth I] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain SB [auth L] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain NB [auth K] MOL2 format, chain JA [auth E] MOL2 format, chain IB [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth I] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain SB [auth L] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain NB [auth K] mmCIF format, chain JA [auth E] mmCIF format, chain IB [auth J] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth I]	DB [auth I] EA [auth D] IB [auth J] JA [auth E] NB [auth K] DB [auth I], EA [auth D], IB [auth J], JA [auth E], NB [auth K], OA [auth F], P [auth A], SB [auth L], TA [auth G], U [auth B], YA [auth H], Z [auth C]	CU-O-CU LINKAGE Cu₂ O BERDEBHAJNAUOM-UHFFFAOYSA-N		Interactions Focus chain DB [auth I] Focus chain EA [auth D] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain NB [auth K] Focus chain OA [auth F] Focus chain P [auth A] Focus chain SB [auth L] Focus chain TA [auth G] Focus chain U [auth B] Focus chain YA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain DB [auth I] Focus chain EA [auth D] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain NB [auth K] Focus chain OA [auth F] Focus chain P [auth A] Focus chain SB [auth L] Focus chain TA [auth G] Focus chain U [auth B] Focus chain YA [auth H] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain V [auth B] SDF format, chain UA [auth G] SDF format, chain TB [auth L] SDF format, chain Q [auth A] SDF format, chain PA [auth F] SDF format, chain OB [auth K] SDF format, chain KA [auth E] SDF format, chain JB [auth J] SDF format, chain FA [auth D] SDF format, chain EB [auth I] SDF format, chain AA [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain TB [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain OB [auth K] MOL2 format, chain KA [auth E] MOL2 format, chain JB [auth J] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth I] MOL2 format, chain AA [auth C] mmCIF format, chain ZA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain TB [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain OB [auth K] mmCIF format, chain KA [auth E] mmCIF format, chain JB [auth J] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth I] mmCIF format, chain AA [auth C]	AA [auth C] EB [auth I] FA [auth D] JB [auth J] KA [auth E] AA [auth C], EB [auth I], FA [auth D], JB [auth J], KA [auth E], OB [auth K], PA [auth F], Q [auth A], TB [auth L], UA [auth G], V [auth B], ZA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EB [auth I] Focus chain FA [auth D] Focus chain JB [auth J] Focus chain KA [auth E] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain TB [auth L] Focus chain UA [auth G] Focus chain V [auth B] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain EB [auth I] Focus chain FA [auth D] Focus chain JB [auth J] Focus chain KA [auth E] Focus chain OB [auth K] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain TB [auth L] Focus chain UA [auth G] Focus chain V [auth B] Focus chain ZA [auth H]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain XA [auth H] SDF format, chain X [auth C] SDF format, chain WA [auth H] SDF format, chain W [auth C] SDF format, chain VA [auth H] SDF format, chain T [auth B] SDF format, chain SA [auth G] SDF format, chain S [auth B] SDF format, chain RB [auth L] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain QB [auth L] SDF format, chain QA [auth G] SDF format, chain PB [auth L] SDF format, chain O [auth A] SDF format, chain NA [auth F] SDF format, chain N [auth A] SDF format, chain MB [auth K] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain LB [auth K] SDF format, chain LA [auth F] SDF format, chain KB [auth K] SDF format, chain IA [auth E] SDF format, chain HB [auth J] SDF format, chain HA [auth E] SDF format, chain GB [auth J] SDF format, chain GA [auth E] SDF format, chain FB [auth J] SDF format, chain DA [auth D] SDF format, chain CB [auth I] SDF format, chain CA [auth D] SDF format, chain BB [auth I] SDF format, chain BA [auth D] SDF format, chain AB [auth I] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain RB [auth L] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain QB [auth L] MOL2 format, chain QA [auth G] MOL2 format, chain PB [auth L] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth K] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth K] MOL2 format, chain LA [auth F] MOL2 format, chain KB [auth K] MOL2 format, chain IA [auth E] MOL2 format, chain HB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain DA [auth D] MOL2 format, chain CB [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain AB [auth I] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain RB [auth L] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain QB [auth L] mmCIF format, chain QA [auth G] mmCIF format, chain PB [auth L] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth K] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth K] mmCIF format, chain LA [auth F] mmCIF format, chain KB [auth K] mmCIF format, chain IA [auth E] mmCIF format, chain HB [auth J] mmCIF format, chain HA [auth E] mmCIF format, chain GB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain DA [auth D] mmCIF format, chain CB [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain AB [auth I]	AB [auth I] BA [auth D] BB [auth I] CA [auth D] CB [auth I] AB [auth I], BA [auth D], BB [auth I], CA [auth D], CB [auth I], DA [auth D], FB [auth J], GA [auth E], GB [auth J], HA [auth E], HB [auth J], IA [auth E], KB [auth K], LA [auth F], LB [auth K], M [auth A], MA [auth F], MB [auth K], N [auth A], NA [auth F], O [auth A], PB [auth L], QA [auth G], QB [auth L], R [auth B], RA [auth G], RB [auth L], S [auth B], SA [auth G], T [auth B], VA [auth H], W [auth C], WA [auth H], X [auth C], XA [auth H], Y [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain PB [auth L] Focus chain QA [auth G] Focus chain QB [auth L] Focus chain R [auth B] Focus chain RA [auth G] Focus chain RB [auth L] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C] Interactions & Density Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth K] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain PB [auth L] Focus chain QA [auth G] Focus chain QB [auth L] Focus chain R [auth B] Focus chain RA [auth G] Focus chain RB [auth L] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Focus chain XA [auth H] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.222 (Depositor), 0.222 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.494	α = 117.04
b = 163.456	β = 95.74
c = 164.352	γ = 107.23

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
CrystalClear	data collection
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-04-28

Deposition Author(s):

This entry supersedes: 2G23

Revision History (Full details and data files)

Version 1.0: 2009-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Derived calculations, Refinement description, Version format compliance
Version 1.2: 2018-04-04
Changes: Data collection
Version 1.3: 2019-07-24
Changes: Data collection, Refinement description
Version 1.4: 2021-10-13
Changes: Database references, Derived calculations
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description