3gyr

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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phenoxazinone synthase

Streptomyces antibioticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	COPPER (II) ION × 18 CU-O-CU LINKAGE × 6 GLYCEROL × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	COPPER (II) ION × 18 CU-O-CU LINKAGE × 6 GLYCEROL × 6 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 6 CU-O-CU LINKAGE × 2 GLYCEROL × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 6 CU-O-CU LINKAGE × 2 GLYCEROL × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 6 CU-O-CU LINKAGE × 2 GLYCEROL × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 6 CU-O-CU LINKAGE × 2 GLYCEROL × 2 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 6 CU-O-CU LINKAGE × 2 GLYCEROL × 2 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 6 CU-O-CU LINKAGE × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHSA_STRAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–612； UniProt 32–643 Author chain B； PDBConstruct 1–612； UniProt 32–643 Author chain C； PDBConstruct 1–612； UniProt 32–643 Author chain D； PDBConstruct 1–612； UniProt 32–643 Author chain E； PDBConstruct 1–612； UniProt 32–643 Author chain F； PDBConstruct 1–612； UniProt 32–643 Author chain G； PDBConstruct 1–612； UniProt 32–643 Author chain H； PDBConstruct 1–612； UniProt 32–643 Author chain I； PDBConstruct 1–612； UniProt 32–643 Author chain J； PDBConstruct 1–612； UniProt 32–643 Author chain K； PDBConstruct 1–612； UniProt 32–643 Author chain L； PDBConstruct 1–612； UniProt 32–643

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gyr
Deposition date deposition_date	2009-04-05
Structure title title	Structure of Phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center.
Keywords keywords	METALLOPROTEIN, LACCASE, MULTICOPPER OXIDASE, HEXAMER, OXIDOREDUCTASE, Antibiotic biosynthesis, Metal-binding; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3gyr__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gyr__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gyr__assembly_6__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.91 Å
Rg (electron density)	32.38 Å
Total Rg	32.91 Å
Atom count	9144
Residues	1174
Excluded volume	161130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gyr__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gyr__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gyr__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3gyr__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3gyr__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3gyr__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3gyr__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3gyr__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Phenoxazinone synthase
Molecular weight formula_weight	67094.1 kDa
EC 编号 ec_number	1.-.-.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	59241

EREQAPAPGELTPFAAPLTVPPVLRPASDEVTRETEIALRPTWVRLHPQLPPTLMWGYDGQVPGPTIEVRRGQRVRIAWTNRIPKGSEYPVTSVEVPLGPPGTPAPNTEPGRGGVEPNKDVAALPAWSVTHLHGAQTGGGNDGWADNAVGFGDAQLSEYPNDHQATQWWYHDHAMNITRWNVMAGLYGTYLVRDDEEDALGLPSGDREIPLLIADRNLDTDEDGRLNGRLLHKTVIVQQSNPETGKPVSIPFFGPYTTVNGRIWPYADVDDGWYRLRLVNASNARIYNLVLIDEDDRPVPGVVHQIGSDGGLLPRPVPVDFDDTLPVLSAAPAERFDLLVDFRALGGRRLRLVDKGPGAPAGTPDPLGGVRYPEVMEFRVRETCEEDSFALPEVLSGSFRRMSHDIPHGHRLIVLTPPGTKGSGGHPEIWEMAEVEDPADVQVPAEGVIQVTGADGRTKTYRRTARTFNDGLGFTIGEGTHEQWTFLNLSPILHPMHIHLADFQVLGRDAYDASGFDLALGGTRTPVRLDPDTPVPLAPNELGHKDVFQVPGPQGLRVMGKFDGAYGRFMYHCHLLEHEDMGMMRPFVVMPPEALKFDHGGAHGGHGEGHTG

Source Source

Source organism organism	Streptomyces antibioticus
NCBI taxonomy ID ncbi_taxonomy_id	1890
Host organism host_organism	STREPTOMYCES LIVIDANS

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 3 Entity 3 non-polymer

Description description	CU-O-CU LINKAGE
Molecular weight formula_weight	143.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4377

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6. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

Domain ID domain_id	3gyrA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrC03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrD03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrE03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrF03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrG03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrH03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrI03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrJ01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrJ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrJ03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrK02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrK03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3gyrL03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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Unit-cell length a length_a	109.494 Å
Unit-cell length b length_b	163.456 Å
Unit-cell length c length_c	164.352 Å
Unit-cell angle α angle_alpha	117.04 °
Unit-cell angle β angle_beta	95.74 °
Unit-cell angle γ angle_gamma	107.23 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1674
R_work r_work	0.1645
R_free r_free	0.2224

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phenoxazinone synthase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gyr__assembly_6__model_1

3gyr__assembly_6__model_1 | I(q)

3gyr__assembly_6__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Phenoxazinone synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3gyr__assembly_6__model_1

3gyr__assembly_6__model_1 | I(q)

3gyr__assembly_6__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

7. Citations (1)