SAXSdb — 9t54

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

Coproheme decarboxylase

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	1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHDC_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–254； UniProt 1–251 Author chain B； PDBConstruct 4–254； UniProt 1–251 Author chain C； PDBConstruct 4–254； UniProt 1–251 Author chain D； PDBConstruct 4–254； UniProt 1–251 Author chain E； PDBConstruct 4–254； 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	9t54
Deposition date deposition_date	2025-11-04
Last revision last_revision	2026-05-13
Structure title title	Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III
Keywords keywords	coproheme, heme, heme b, heme biosynthesis, mmd, iron, coproporphyrin, enzyme, decarboxylase, 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.

9t54__assembly_1__model_1

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

Download this curve (.dat)

9t54__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9t54__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.54 Å
Rg (electron density)	31.11 Å
Total Rg	32.10 Å
Atom count	10291
Residues	1240
Excluded volume	183180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9t54__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 (3)

Entity 1 Entity 1 polymer

Description description	Coproheme decarboxylase
Molecular weight formula_weight	29040.9 kDa
EC 编号 ec_number	1.3.98.5
Mutation mutation	H117A
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	10326

GPAMNEAVKTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYLASAMAGGDDPYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI

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	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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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Unit-cell length a length_a	78.429 Å
Unit-cell length b length_b	129.300 Å
Unit-cell length c length_c	78.651 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.05 °
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	—

Resolution resolution	2.194 Å
Low-resolution limit resolution_low	65.254 Å
R factor r_factor	—
R_work r_work	0.1804
R_free r_free	0.2061

Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III

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

Coproheme decarboxylase

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

9t54__assembly_1__model_1

9t54__assembly_1__model_1 | I(q)

9t54__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III

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

Coproheme decarboxylase

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

9t54__assembly_1__model_1

9t54__assembly_1__model_1 | I(q)

9t54__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)