PDB-9qq5: Mini-bacterioferritin from Candidatus Methanoperedens species BLZ...

ID or keywords:

Entry

Database: PDB / ID: 9qq5

Title

Mini-bacterioferritin from Candidatus Methanoperedens species BLZ2 in a partially oxidized state

Components

Bacterioferritin

Keywords

OXIDOREDUCTASE / ferritin-like protein / mini-ferritin / Fe-coproporphyrin III / anaerobic methane-oxidising archaea / archaea / iron homeostasis / iron storage / dodecamer / nano-compartment

Function / homology

: / Chem-FEC

Function and homology information

Biological species

Candidatus Methanoperedens sp. BLZ2 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.54 Å

Authors

Wissink, M. / Wagner, T.

Funding support

European Union,

Germany,

Netherlands, 6items

Organization	Grant number	Country
European Research Council (ERC)	101125699	European Union
Max Planck Society		Germany
German Research Foundation (DFG)	WA 4053/1-1	Germany
Netherlands Organisation for Scientific Research (NWO)	024.002.002	Netherlands
Netherlands Organisation for Scientific Research (NWO)	VI.Vidi.223.012	Netherlands
European Research Council (ERC)	854088	European Union

Citation

Journal: Commun Biol / Year: 2026
Title: Mini-bacterioferritins: structural insight into a ferritin-like protein from the anaerobic methane-oxidising archaeon Candidatus Methanoperedens carboxydivorans.
Authors: Wissink, M. / Engilberge, S. / Leao, P. / Jansen, R.S. / Jetten, M.S.M. / Belhamri, M. / Lemaire, O.N. / Royant, A. / Welte, C.U. / Wagner, T.

History

Deposition	Mar 31, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 1, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 27, 2026	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qq5.cif.gz	262.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9qq5.ent.gz	213.2 KB	Display	PDB format
PDBx/mmJSON format	9qq5.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/qq/9qq5 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/9qq5	HTTPS FTP

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Related structure data

Related structure data	9qq4C 9qqhC 9qqiC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bacterioferritin

C: Bacterioferritin

E: Bacterioferritin

G: Bacterioferritin

hetero molecules

67.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bacterioferritin

C: Bacterioferritin

E: Bacterioferritin

G: Bacterioferritin

hetero molecules

A: Bacterioferritin

C: Bacterioferritin

E: Bacterioferritin

G: Bacterioferritin

hetero molecules

A: Bacterioferritin

C: Bacterioferritin

E: Bacterioferritin

G: Bacterioferritin

hetero molecules

defined by author&software
Evidence: native gel electrophoresis, The native gel electrophoresis confirms the dodecameric assembly in solution
203 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.752, 122.752, 122.752
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	C-473- HOH
2	1	C-497- HOH
3	1	C-500- HOH
4	1	G-452- HOH

#1: Protein	Bacterioferritin Mass: 15969.113 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: Mini-bacterioferritin from Candidatus Methanoperedens species BLZ2 Source: (natural) Candidatus Methanoperedens sp. BLZ2 (archaea) Cell line: / / Organ: / / Plasmid details: / / Strain: BLZ2 / Tissue: /
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 4 / Source method: isolated from a natural source / Formula: C₃₆H₃₆FeN₄O₈ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.46 Å³/Da / Density % sol: 50.11 % Description: Triangular pink plates becoming brownish upon oxidation
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Crystals were obtained on a Junior Clover plate (Jena Bioscience, Germany) under an anaerobic atmosphere of 97:3% N2:H2. The crystallization reservoir (100 ul) contained 20% w/v Polyethylene ...Details: Crystals were obtained on a Junior Clover plate (Jena Bioscience, Germany) under an anaerobic atmosphere of 97:3% N2:H2. The crystallization reservoir (100 ul) contained 20% w/v Polyethylene glycol 3,350 and 200 mM tri-Potassium citrate. 1 ul of purified protein solution at 22 mg/mL in 25 mM Tris/HCl, 10% v/v glycerol and 2 mM dithiothreitol was mixed with 1 ul of the crystallization solution. The crystal was exposed to air for 10 min, and was then soaked in the crystallization solution supplemented with 20% v/v glycerol prior freezing.

Crystal

Density Matthews: 2.46 Å³/Da / Density % sol: 50.11 %
Description: Triangular pink plates becoming brownish upon oxidation

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals were obtained on a Junior Clover plate (Jena Bioscience, Germany) under an anaerobic atmosphere of 97:3% N2:H2. The crystallization reservoir (100 ul) contained 20% w/v Polyethylene ...

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: / / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.537→86.799 Å / Num. obs: 91535 / % possible obs: 100 % / Redundancy: 10.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.158 / R_pim(I) all: 0.051 / R_rim(I) all: 0.166 / Net I/σ(I): 7.5
Reflection shell	Resolution: 1.537→1.563 Å / Redundancy: 5.8 % / R_merge(I) obs: 1.851 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4547 / CC_1/2: 0.371 / R_pim(I) all: 0.83 / R_rim(I) all: 2.034 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.54→38.82 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.03 / Stereochemistry target values: ML
Details: The model was manually optimised with Coot. Refinement was performed in Phenix refine without applying non-crystallography symmetry and by using a translation-libration screw. The model was ...

	R_factor	Num. reflection	% reflection
R_free	0.1816	4353	4.77 %
R_work	0.1655	-	-
obs	0.1663	91188	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 24 Å²

Refinement step

Cycle: LAST / Resolution: 1.54→38.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4397	0	212	838	5447

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4896
X-RAY DIFFRACTION	f_angle_d	0.89	6682
X-RAY DIFFRACTION	f_dihedral_angle_d	15.418	1963
X-RAY DIFFRACTION	f_chiral_restr	0.052	688
X-RAY DIFFRACTION	f_plane_restr	0.008	856

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 (%)
1.54-1.55	0.3006	142	0.2886	2766	X-RAY DIFFRACTION	96
1.55-1.57	0.2878	152	0.2782	2775	X-RAY DIFFRACTION	98
1.57-1.59	0.2794	158	0.2506	2845	X-RAY DIFFRACTION	100
1.59-1.61	0.3036	131	0.2454	2885	X-RAY DIFFRACTION	100
1.61-1.63	0.2613	174	0.2336	2866	X-RAY DIFFRACTION	100
1.63-1.66	0.2649	161	0.2316	2867	X-RAY DIFFRACTION	100
1.66-1.68	0.239	176	0.2171	2812	X-RAY DIFFRACTION	100
1.68-1.7	0.2354	146	0.2095	2930	X-RAY DIFFRACTION	100
1.7-1.73	0.2306	134	0.2082	2886	X-RAY DIFFRACTION	100
1.73-1.76	0.2342	140	0.2043	2886	X-RAY DIFFRACTION	100
1.76-1.79	0.2261	145	0.2016	2905	X-RAY DIFFRACTION	100
1.79-1.82	0.2204	130	0.1919	2892	X-RAY DIFFRACTION	100
1.82-1.86	0.2233	141	0.1899	2881	X-RAY DIFFRACTION	100
1.86-1.89	0.2198	143	0.2024	2885	X-RAY DIFFRACTION	100
1.89-1.94	0.2296	158	0.2288	2883	X-RAY DIFFRACTION	100
1.94-1.98	0.2415	131	0.1907	2924	X-RAY DIFFRACTION	100
1.98-2.03	0.2042	137	0.1712	2858	X-RAY DIFFRACTION	100
2.03-2.09	0.1763	121	0.1582	2951	X-RAY DIFFRACTION	100
2.09-2.15	0.1895	150	0.158	2884	X-RAY DIFFRACTION	100
2.15-2.22	0.1872	116	0.1654	2924	X-RAY DIFFRACTION	100
2.22-2.29	0.1906	151	0.1903	2881	X-RAY DIFFRACTION	99
2.3-2.39	0.1613	147	0.1481	2906	X-RAY DIFFRACTION	100
2.39-2.5	0.1718	171	0.1435	2873	X-RAY DIFFRACTION	100
2.5-2.63	0.1881	125	0.1504	2928	X-RAY DIFFRACTION	100
2.63-2.79	0.1764	156	0.1508	2909	X-RAY DIFFRACTION	100
2.79-3.01	0.1466	135	0.1385	2916	X-RAY DIFFRACTION	100
3.01-3.31	0.1593	139	0.1464	2958	X-RAY DIFFRACTION	100
3.31-3.79	0.158	145	0.1408	2925	X-RAY DIFFRACTION	100
3.79-4.77	0.1066	135	0.1157	2983	X-RAY DIFFRACTION	100
4.77-38.82	0.173	163	0.1781	3051	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	8.158	3.8352	7.5006	2.793	3.7825	7.7318	0.2528	0.072	-0.4365	0.1735	0.0432	-0.1856	0.413	0.1521	-0.392	0.1808	0.042	0.0212	0.1361	-0.0068	0.2052	-16.4629	-61.5886	34.2337
2	4.3766	3.5214	3.3176	3.3258	2.3869	2.6763	0.0354	-0.198	-0.0646	0.1439	-0.0332	0.0059	0.108	-0.0138	0.002	0.1583	0.0278	0.0247	0.1376	0.0152	0.1768	-19.5818	-55.2047	38.2191
3	4.298	3.284	3.4721	3.464	3.4081	3.9373	-0.0455	0.2189	-0.1779	-0.0893	0.1451	-0.0822	-0.0313	0.2292	-0.1404	0.1331	0.0118	0.0209	0.1356	-0.0191	0.1548	-12.0128	-47.3249	11.8879
4	5.8069	6.7468	4.4271	7.8306	5.1409	3.37	-0.0177	-0.0971	0.2537	-0.0083	-0.192	0.3419	-0.0213	-0.1027	0.1905	0.1363	0.0077	0.005	0.1591	-0.0249	0.1813	-19.3449	-43.7614	13.8713
5	4.8686	5.279	2.1452	6.1552	2.2881	1.074	-0.2732	0.1961	-0.5656	-0.1318	0.2729	-0.532	0.0568	0.1232	-0.0313	0.1786	0.0125	0.0214	0.1827	-0.0681	0.2415	-16.579	-57.7178	10.3746
6	5.0508	0.1476	2.5206	0.3655	-0.3723	2.0236	0.0904	0.3007	-0.2088	-0.1019	-0.0032	-0.1022	0.1976	0.244	-0.1006	0.1635	0.0173	0.0363	0.1885	-0.0528	0.1815	-9.7381	-43.9285	3.8298
7	6.5548	2.8448	1.3588	2.2947	0.6698	1.2507	-0.0545	0.2706	0.0285	-0.0954	0.0886	0.0628	0.0019	0.0068	-0.0324	0.1496	0.011	0.0222	0.1659	-0.0249	0.1253	-17.2892	-38.1287	3.1397
8	3.8544	-3.1179	-1.6561	4.3726	1.8126	1.0635	0.1276	0.3346	-0.0464	-0.2246	-0.188	-0.0375	-0.08	-0.1116	0.0166	0.1797	-0.0243	0.0078	0.1835	0.0212	0.1156	-25.2697	-15.0378	-0.9032
9	5.4152	-3.0988	-2.18	2.3216	1.403	1.3637	-0.0626	0.0715	-0.1517	-0.0027	0.0093	0.1114	0.0027	0.0115	0.0589	0.161	-0.0191	-0.0059	0.1603	0.0008	0.1255	-28.8898	-17.6042	5.5742
10	6.0082	-4.5356	1.2914	3.6207	-0.536	1.2559	0.0071	0.2217	0.1424	-0.2294	-0.0487	-0.1359	-0.0944	0.1217	0.0269	0.2608	-0.0241	-0.0047	0.236	0.0391	0.1796	-28.0434	-6.4793	-1.8571
11	2.9917	-3.5825	-1.725	5.935	2.4376	1.4166	0.1514	0.262	0.1189	-0.437	-0.0959	-0.1217	-0.1772	-0.0673	-0.0389	0.2211	-0.0197	-0.0036	0.2383	0.0249	0.1263	-32.5232	-19.585	-7.6679
12	6.7564	-5.1844	-1.3478	5.9946	1.4556	1.2407	-0.0054	0.2278	-0.1602	-0.1271	-0.0147	0.1377	0.0444	-0.0401	0.0013	0.1639	-0.0356	0.002	0.1903	-0.0055	0.108	-34.2991	-25.371	-2.3464
13	2.419	-2.4137	-0.083	3.3167	0.0816	0.5631	-0.0527	0.0283	0.0681	0.0322	0.0612	-0.0767	-0.1207	0.0351	0.003	0.1677	-0.0323	0.0035	0.1662	-0.0007	0.1384	-19.4536	-8.2421	12.7447
14	0.6977	-0.1766	-0.1353	1.035	0.2613	0.9688	0.0013	0.0606	0.0723	-0.0349	0.0398	-0.0938	-0.1144	0.0826	-0.077	0.1774	-0.0375	0.0153	0.1715	0.0008	0.1652	-13.4474	-2.8162	17.7639
15	7.0922	1.4924	4.0407	1.0824	1.0095	3.9638	0.0183	-0.0066	-0.4437	0.0689	0.1063	-0.1559	0.1182	0.1071	-0.1791	0.1605	0.0247	0.0295	0.1334	-0.0184	0.195	-13.3364	-55.7926	25.8001
16	6.561	2.1068	1.9912	1.1145	0.5812	0.7901	0.0434	-0.1695	0.1824	0.052	-0.0431	0.0552	0.0379	-0.0345	0.0499	0.1553	0.0098	0.0143	0.1541	-0.0072	0.1655	-19.7279	-51.0002	26.6108
17	4.8338	6.223	1.5467	8.4119	1.3111	2.1548	0.2351	0.1839	-0.587	0.1199	-0.0253	-0.508	0.3486	0.2246	-0.1637	0.2572	0.0553	-0	0.2033	-0.0345	0.2478	-16.1532	-61.7815	19.711

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'G' and (resid 80 through 107 )
2	X-RAY DIFFRACTION	2	chain 'G' and (resid 108 through 138 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 2 through 34 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 35 through 63 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 64 through 73 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 74 through 107 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 108 through 139 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 2 through 29 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 30 through 68 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 69 through 79 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 80 through 107 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 108 through 138 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 2 through 68 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 69 through 137 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 2 through 29 )
16	X-RAY DIFFRACTION	16	chain 'G' and (resid 30 through 68 )
17	X-RAY DIFFRACTION	17	chain 'G' and (resid 69 through 79 )

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