PDB-9t54: Coproheme decarboxylase H117A mutant from Listeria monocytogenes ...

ID or keywords:

Entry

Database: PDB / ID: 9t54

Title

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

Components

Coproheme decarboxylase

Keywords

OXIDOREDUCTASE / coproheme / heme / heme b / heme biosynthesis / mmd / iron / coproporphyrin / enzyme / decarboxylase

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / heme B biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function

Biological species

Listeria monocytogenes EGD-e (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.194 Å

Authors

Falb, N. / Hofbauer, S.

Funding support

1items

Citation

Journal: To Be Published
Title: Coproheme decarboxylase H117A mutant from Listeria monocytogenes in complex with iron coproporphyrin III
Authors: Falb, N. / Hofbauer, S.

History

Deposition	Nov 4, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 13, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9t54.cif.gz	267.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9t54.ent.gz	211.6 KB	Display	PDB format
PDBx/mmJSON format	9t54.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t5/9t54 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/9t54	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Coproheme decarboxylase

B: Coproheme decarboxylase

C: Coproheme decarboxylase

D: Coproheme decarboxylase

E: Coproheme decarboxylase

hetero molecules

149 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry, light scattering

Unit cell

Length a, b, c (Å)	78.429, 129.3, 78.651
Angle α, β, γ (deg.)	90, 106.048, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ILE	ILE	A	A	3 - 251	6 - 254
2	1	1	ILE	ILE	B	B	3 - 251	6 - 254
3	2	2	THR	THR	A	A	3 - 250	6 - 253
4	2	2	THR	THR	C	C	3 - 250	6 - 253
5	3	3	ILE	ILE	A	A	3 - 251	6 - 254
6	3	3	ILE	ILE	D	D	3 - 251	6 - 254
7	4	4	ILE	ILE	A	A	3 - 251	6 - 254
8	4	4	ILE	ILE	E	E	3 - 251	6 - 254
9	5	5	ILE	ILE	B	B	3 - 251	6 - 254
10	5	5	ILE	ILE	C	C	3 - 251	6 - 254
11	6	6	ILE	ILE	B	B	3 - 251	6 - 254
12	6	6	ILE	ILE	D	D	3 - 251	6 - 254
13	7	7	ILE	ILE	B	B	3 - 251	6 - 254
14	7	7	ILE	ILE	E	E	3 - 251	6 - 254
15	8	8	THR	THR	C	C	3 - 250	6 - 253
16	8	8	THR	THR	D	D	3 - 250	6 - 253
17	9	9	THR	THR	C	C	3 - 250	6 - 253
18	9	9	THR	THR	E	E	3 - 250	6 - 253
19	10	10	ILE	ILE	D	D	3 - 251	6 - 254
20	10	10	ILE	ILE	E	E	3 - 251	6 - 254

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

#1: Protein	Coproheme decarboxylase / Coproheme III oxidative decarboxylase / Hydrogen peroxide-dependent heme synthase / LmCld Mass: 29040.900 Da / Num. of mol.: 5 / Mutation: H117A Source method: isolated from a genetically manipulated source Details: Homopentameric Coproheme decarboxylase GPA in beginning is from protease cleavage N term not resolved all chains contain same molecule Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria) Gene: chdC, hemQ, lmo2113 / Plasmid: pETM11 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8Y5F1, hydrogen peroxide-dependent heme synthase
#2: Chemical	ChemComp-FEC / 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONIC ACID FERROUS COMPLEX / FE-COPROPORPHYRIN III Mass: 708.538 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃₆H₃₆FeN₄O₈ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.5 % / Description: plates
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium iodide 20 % w/v PEG 3350 1 mM Cyanide 5 mg/mL protein

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-3 / Wavelength: 0.9677 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 25, 2025

Radiation

Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9677 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.7491
pseudo-merohedral	2	2	-L, -K, -H	2	0.2509

Reflection

Resolution: 2.19→65.254 Å / Num. obs: 76424 / % possible obs: 98.51 % / Redundancy: 7.2 % / B_iso Wilson estimate: 36.2 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.3247 / R_pim(I) all: 0.129 / R_rim(I) all: 0.3498 / Net I/σ(I): 6.92

Reflection shell

Resolution: 2.19→2.268 Å / Redundancy: 7.4 % / R_merge(I) obs: 2.636 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 56392 / CC_1/2: 0.405 / R_pim(I) all: 1.028 / R_rim(I) all: 2.832 / % possible all: 96.78

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431 (refmacat 0.4.105)	refinement
Aimless	0.8.2	data scaling
DIALS	3.23.0-g7aff524e7-release	data reduction
gemmi	0.7.1	data extraction
PHASER	2.8.3	phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.194→65.254 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.939 / SU B: 2.465 / SU ML: 0.069 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.038 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2061	1754	-	RANDOM
R_work	0.1804	73658	-	-
all	0.183	-	-	-
obs	-	76213	97.965 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 44.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-12.214 Å²	-0 Å²	-16.548 Å²
2-	-	35.142 Å²	0 Å²
3-	-	-	-22.928 Å²

Refinement step

Cycle: LAST / Resolution: 2.194→65.254 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10046	0	245	35	10326

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	10570
X-RAY DIFFRACTION	r_angle_refined_deg	1.997	1.855	14358
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.087	5	1234
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.74	5	105
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.877	10	1761
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.596	10	525
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	1460
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	8371
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	4073
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	7155
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	265
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.336	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	5.639	4.07	4954
X-RAY DIFFRACTION	r_mcangle_it	6.869	7.298	6182
X-RAY DIFFRACTION	r_scbond_it	6.984	4.366	5616
X-RAY DIFFRACTION	r_scangle_it	8.79	7.863	8176
X-RAY DIFFRACTION	r_lrange_it	10.392	47.582	15309
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.085	0.05	7779
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.088	0.05	7918
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.1	0.05	7858
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.081	0.05	7955
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.079	0.05	7816
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.088	0.05	7781
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.084	0.05	7797
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.097	0.05	7871
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.091	0.05	7864
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.081	0.05	8018

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08471	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08471	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08754	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.08754	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10007	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.10007	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08127	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.08127	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.07883	0.0501
5	10	C	X-RAY DIFFRACTION	Local ncs	0.07883	0.0501
6	11	B	X-RAY DIFFRACTION	Local ncs	0.08838	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.08838	0.0501
7	13	B	X-RAY DIFFRACTION	Local ncs	0.08418	0.05009
7	14	E	X-RAY DIFFRACTION	Local ncs	0.08418	0.05009
8	15	C	X-RAY DIFFRACTION	Local ncs	0.09664	0.0501
8	16	D	X-RAY DIFFRACTION	Local ncs	0.09664	0.0501
9	17	C	X-RAY DIFFRACTION	Local ncs	0.09086	0.05009
9	18	E	X-RAY DIFFRACTION	Local ncs	0.09086	0.05009
10	19	D	X-RAY DIFFRACTION	Local ncs	0.08093	0.0501
10	20	E	X-RAY DIFFRACTION	Local ncs	0.08093	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.194-2.251	0.257	99	0.217	4841	X-RAY DIFFRACTION	87.2637
2.251-2.312	0.279	135	0.214	5384	X-RAY DIFFRACTION	99.3698
2.312-2.379	0.27	126	0.201	5146	X-RAY DIFFRACTION	98.7266
2.379-2.452	0.247	114	0.214	5067	X-RAY DIFFRACTION	99.3861
2.452-2.533	0.272	101	0.18	4905	X-RAY DIFFRACTION	98.6404
2.533-2.621	0.238	125	0.194	4768	X-RAY DIFFRACTION	99.5321
2.621-2.72	0.233	103	0.192	4568	X-RAY DIFFRACTION	99.193
2.72-2.831	0.233	100	0.196	4410	X-RAY DIFFRACTION	99.7788
2.831-2.957	0.211	110	0.199	4229	X-RAY DIFFRACTION	99.1092
2.957-3.101	0.236	94	0.195	3994	X-RAY DIFFRACTION	97.7289
3.101-3.268	0.246	95	0.195	3593	X-RAY DIFFRACTION	91.9701
3.268-3.466	0.198	87	0.177	3539	X-RAY DIFFRACTION	97.1337
3.466-3.704	0.19	87	0.174	3441	X-RAY DIFFRACTION	99.8867
3.704-4	0.193	79	0.176	3238	X-RAY DIFFRACTION	100.1812
4-4.38	0.204	63	0.171	2960	X-RAY DIFFRACTION	99.7032
4.38-4.894	0.165	66	0.153	2704	X-RAY DIFFRACTION	100.1808
4.894-5.646	0.196	60	0.166	2377	X-RAY DIFFRACTION	99.959
5.646-6.902	0.311	34	0.207	2023	X-RAY DIFFRACTION	100
6.902-9.707	0.201	37	0.164	1585	X-RAY DIFFRACTION	100.0617
9.707-65.254	0.169	25	0.171	886	X-RAY DIFFRACTION	99.4541

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