SAXSdb — 2ive

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

PROTOPORPHYRINOGEN OXIDASE

MYXOCOCCUS XANTHUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 GLYCEROL × 3 (3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 GLYCEROL × 3 (3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPOX_MYXXA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–478； UniProt 4–471 Author chain B； PDBConstruct 11–478； UniProt 4–471

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	2ive
Deposition date deposition_date	2006-06-13
Structure title title	Structure of protoporphyrinogen oxidase from Myxococcus xanthus
Keywords keywords	;OXIDOREDUCTASE, PROTOPORPHYRINOGEN OXIDASE, PORPHYRIN BIOSYNTHESIS, CHLOROPHYLL BIOSYNTHESIS, FAD, PORPHYRIA, FLAVOPROTEIN, HEME BIOSYNTHESIS, HAEM BIOSYNTHESIS ;; 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.

2ive__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ive__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ive__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.15 Å
Rg (electron density)	23.14 Å
Total Rg	24.06 Å
Atom count	3443
Residues	450
Excluded volume	61351 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ive__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ive__assembly_2__model_1`	monomeric （1）	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	PROTOPORPHYRINOGEN OXIDASE
Molecular weight formula_weight	50396.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7011

MDHHHHHHHHMPRTTGMNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQAALPAGTAPKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVAGNTSHAP

Source Source

Source organism organism	MYXOCOCCUS XANTHUS
NCBI taxonomy ID ncbi_taxonomy_id	34
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE
Molecular weight formula_weight	354.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ivea1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d2ivea2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.5 — L-aminoacid/polyamine oxidase

Domain ID domain_id	d2iveb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d2iveb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.5 — L-aminoacid/polyamine oxidase

CATH v4.4 (6 domains)

Domain ID domain_id	2iveA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2iveA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — Protoporphyrinogen oxidase, mitochondrial; domain 2

Domain ID domain_id	2iveA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3110 — protoporphyrinogen ix oxidase, domain 3
Homologous superfamily homologous superfamily	10 — protoporphyrinogen ix oxidase, domain 3

Domain ID domain_id	2iveB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2iveB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — Protoporphyrinogen oxidase, mitochondrial; domain 2

Domain ID domain_id	2iveB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3110 — protoporphyrinogen ix oxidase, domain 3
Homologous superfamily homologous superfamily	10 — protoporphyrinogen ix oxidase, domain 3

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Unit-cell length a length_a	148.566 Å
Unit-cell length b length_b	148.566 Å
Unit-cell length c length_c	132.745 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	74.330 Å
R factor r_factor	0.2480
R_work r_work	0.2470
R_free r_free	0.2870

Structure of protoporphyrinogen oxidase from Myxococcus xanthus

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

PROTOPORPHYRINOGEN OXIDASE

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

2ive__assembly_2__model_1

2ive__assembly_2__model_1 | I(q)

2ive__assembly_2__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of protoporphyrinogen oxidase from Myxococcus xanthus

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

PROTOPORPHYRINOGEN OXIDASE

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

2ive__assembly_2__model_1

2ive__assembly_2__model_1 | I(q)

2ive__assembly_2__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)