← Back to search

9t54

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

Method: X-RAY DIFFRACTION D_max: 90.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9t54
deposition_date	2025-11-04
last_revision	2026-05-13
title	Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III
keywords	coproheme, heme, heme b, heme biosynthesis, mmd, iron, coproporphyrin, enzyme, decarboxylase, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.54 Å
rg_electron	31.11 Å
i0	319390000.00
molecular_weight	145760.0 kDa
excluded_volume	183180 Å³
envelope_volume	228000 Å³
shell_volume	56986 Å³
envelope_diameter	97.5 Å
shell_rg	40.99 Å
envelope_rg	30.83 Å
shape_rg	31.05 Å
total_rg	32.10 Å
total_atoms	10291
n_residues	1240
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	90.3 Å
rg_real	32.20 Å
rg_real_error	0.32 Å
i0_real	3.1940e+08
i0_real_error	4.3710e+06
rg_reciprocal	32.35 Å
i0_reciprocal	319400000.0000
total_estimate	0.9023
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	44.2 Å
skewness	-0.005
kurtosis	-0.527
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	318500000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.849

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Coproheme decarboxylase
formula_weight	29040.9 kDa
ec_number	1.3.98.5
mutation	H117A
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	10326

GPAMNEAVKTLDGWFCLHDFRSIDWAAWRELNPGNQELMLNELSHFLSDMEITKNIGEGEHTIYSILGQKADLVFFTLRDSLEALNEVENRFNKLAIADYLLPTYSYISVVELSNYLASAMAGGDDPYQNKGVRARLYPALPPKKHICFYPMSKKRDGADNWYMLPMEERQQLIRDHGLIGRSYAGKVQQIIGGSIGFDDYEWGVTLFSDDALEFKRIVTEMRFDEASARYAEFGSFFIGNLLLSEQLSKLFTI

Source

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

Entity 2 non-polymer

description	1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX
formula_weight	708.5 kDa
src_method	syn
entity_count	5

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	35

▶

6. Citations (1)

▶

length_a	78.429 Å
length_b	129.300 Å
length_c	78.651 Å
angle_alpha	90.00 °
angle_beta	106.05 °
angle_gamma	90.00 °
z_pdb	10

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.194 Å
resolution_low	65.254 Å
r_factor	—
r_work	0.1804
r_free	0.2061

fit	/app/data/saxs_computation/t5/9t54/9t54.fit
pddf	/app/data/pr_computation/t5/9t54/9t54.pr.out
profile	/app/data/saxs_computation/t5/9t54/9t54.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction