6fxj

Structure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III

Method: X-RAY DIFFRACTION

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

Putative heme-dependent peroxidase lmo2113

Listeria monocytogenes EGD-e

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	SODIUM ION × 7 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX × 5 N-PROPANOL × 10 CHLORIDE ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y2113_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–251； UniProt 1–251 Author chain B； PDBConstruct 1–251； UniProt 1–251 Author chain C； PDBConstruct 1–251； UniProt 1–251 Author chain D； PDBConstruct 1–251； UniProt 1–251 Author chain E； PDBConstruct 1–251； UniProt 1–251

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	6fxj
Deposition date deposition_date	2018-03-09
Structure title title	Structure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III
Keywords keywords	coproheme binding, coproheme decarboxylase, pentamer, oxidoreductase; 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.

6fxj__assembly_1__model_1

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

Download this curve (.dat)

6fxj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fxj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.06 Å
Rg (electron density)	30.64 Å
Total Rg	31.64 Å
Atom count	19820
Residues	1212
Excluded volume	181480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fxj__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Putative heme-dependent peroxidase lmo2113
Molecular weight formula_weight	28882.7 kDa
EC 编号 ec_number	1.11.1.-
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	21321

MNEAVKTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYLASHMAGGDDPYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI

Source Source

Source organism organism	Listeria monocytogenes EGD-e
NCBI taxonomy ID ncbi_taxonomy_id	169963
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
Molecular weight formula_weight	708.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	N-PROPANOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1100

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6fxja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d6fxjb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d6fxjc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d6fxjd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

Domain ID domain_id	d6fxje_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	6fxjA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

Domain ID domain_id	6fxjE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1030 — Apc35880; domain 1

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Unit-cell length a length_a	77.870 Å
Unit-cell length b length_b	129.110 Å
Unit-cell length c length_c	77.920 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	1.790 Å
Low-resolution limit resolution_low	48.890 Å
R factor r_factor	0.1869
R_work r_work	0.1865
R_free r_free	0.2137

Structure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III

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

Putative heme-dependent peroxidase lmo2113

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

6fxj__assembly_1__model_1

6fxj__assembly_1__model_1 | I(q)

6fxj__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Structure of coproheme decarboxylase from Listeria monocytogenes in complex with iron coproporphyrin III

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

Putative heme-dependent peroxidase lmo2113

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

6fxj__assembly_1__model_1

6fxj__assembly_1__model_1 | I(q)

6fxj__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)