SAXSdb — 3fmu

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

Versatile peroxidase VPL2

Pleurotus eryngii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 CALCIUM ION × 2 ZINC ION × 8 FE (III) ION × 5 CACODYLATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPL2_PLEER
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–331； UniProt 31–361

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	3fmu
Deposition date deposition_date	2008-12-22
Structure title title	Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii
Keywords keywords	;CLASS II (FUNGAL) PEROXIDASES, protoporphyrin IX, ELECTRON TRANSFER, LIGNIN PEROXIDASE, LIGNIN DEGRADATION, MANGANESE PEROXIDASE, MN-INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS, MNII OXIDATION, PEROXIDASE, POLYVALENT PEROXIDASE, OXIDOREDUCTASE, Heme, Hydrogen peroxide, Iron, Manganese, Metal-binding, Secreted, Zymogen ;; 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.

3fmu__assembly_1__model_1

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

Download this curve (.dat)

3fmu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fmu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.96 Å
Rg (electron density)	18.93 Å
Total Rg	19.85 Å
Atom count	4685
Residues	319
Excluded volume	42927 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fmu__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Versatile peroxidase VPL2
Molecular weight formula_weight	34506.6 kDa
EC 编号 ec_number	1.11.1.16
Mutation mutation	W164S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5405

ATCDDGRTTANAACCILFPILDDIQENLFDGAQCGEEVHESLRLTFHDAIGFSPTLGGGGADGSIIAFDTIETNFPANAGIDEIVSAQKPFVAKHNISAGDFIQFAGAVGVSNCPGGVRIPFFLGRPDAVAASPDHLVPEPFDSVDSILARMGDAGFSPVEVVSLLASHSIAAADKVDPSIPGTPFDSTPGVFDSQFFIETQLKGRLFPGTADNKGEAQSPLQGEIRLQSDHLLARDPQTACEWQSMVNNQPKIQNRFAATMSKMALLGQDKTKLIDCSDVIPTPPALVGAAHLPAGFSLSDVEQACAATPFPALTADPGPVTSVPPVPGS

Source Source

Source organism organism	Pleurotus eryngii
Common name common_name	Boletus of the steppes
NCBI taxonomy ID ncbi_taxonomy_id	5323
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	524

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3fmua_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3fmuA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3fmuA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

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Unit-cell length a length_a	63.199 Å
Unit-cell length b length_b	63.199 Å
Unit-cell length c length_c	99.237 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	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.040 Å
Low-resolution limit resolution_low	44.688 Å
R factor r_factor	0.1115
R_work r_work	0.1109
R_free r_free	0.1230

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

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

Versatile peroxidase VPL2

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

3fmu__assembly_1__model_1

3fmu__assembly_1__model_1 | I(q)

3fmu__assembly_1__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii

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

Versatile peroxidase VPL2

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

3fmu__assembly_1__model_1

3fmu__assembly_1__model_1 | I(q)

3fmu__assembly_1__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)