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

ID or keywords:

Entry

Database: PDB / ID: 9qqi

Title

Mini-bacterioferritin from Candidatus Methanoperedens species BLZ2 untreated control of a redox cycling experiment

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: 1.68 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	9qqi.cif.gz	260.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9qqi.ent.gz	211.3 KB	Display	PDB format
PDBx/mmJSON format	9qqi.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/9qqi ftp://data.pdbj.org/pub/pdb/validation_reports/qq/9qqi	HTTPS FTP

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Related structure data

Related structure data	9qq4C 9qq5C 9qqhC 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

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

hetero molecules

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

1

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

hetero molecules

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

hetero molecules

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: 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)	122.662, 122.662, 122.662
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	B-439- HOH
2	1	D-504- HOH
3	1	D-538- HOH
4	1	D-543- 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-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: obtained synthetically / Formula: C₃₆H₃₆FeN₄O₈ / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.45 Å³/Da / Density % sol: 49.79 % / Description: Triangular pink plates
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) using 100 uL crystallisation solution under an anaerobic atmosphere of 97:3% N2:H2. The crystallization reservoir ...Details: Crystals were obtained on a Junior Clover plate (Jena Bioscience, Germany) using 100 uL crystallisation solution under an anaerobic atmosphere of 97:3% N2:H2. The crystallization reservoir 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 soaked in the crystallization solution supplemented with 20% v/v glycerol prior freezing in the anaerobic chamber.

Crystal

Density Matthews: 2.45 Å³/Da / Density % sol: 49.79 % / Description: Triangular pink plates

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) using 100 uL crystallisation solution under an anaerobic atmosphere of 97:3% N2:H2. The crystallization reservoir ...

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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: 1.677→86.735 Å / Num. obs: 69454 / % possible obs: 98.6 % / Redundancy: 13.4 % / CC_1/2: 0.996 / R_merge(I) obs: 0.206 / R_pim(I) all: 0.058 / R_rim(I) all: 0.214 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.677→1.705 Å / Redundancy: 13.5 % / R_merge(I) obs: 3.719 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3470 / CC_1/2: 0.323 / R_pim(I) all: 1.048 / R_rim(I) all: 3.865 / % 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: 1.68→38.79 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.38 / 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	0.1811	3339	4.82 %
R_work	0.1622	-	-
obs	0.1631	69258	98.3 %

Solvent computation

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

Displacement parameters

B_iso mean: 28.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→38.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4406	0	222	867	5495

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4805
X-RAY DIFFRACTION	f_angle_d	0.869	6535
X-RAY DIFFRACTION	f_dihedral_angle_d	15.589	1915
X-RAY DIFFRACTION	f_chiral_restr	0.051	677
X-RAY DIFFRACTION	f_plane_restr	0.008	827

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 (%)
1.68-1.7	0.3199	136	0.2934	2700	X-RAY DIFFRACTION	97
1.7-1.73	0.3329	143	0.2765	2698	X-RAY DIFFRACTION	98
1.73-1.75	0.2758	133	0.2699	2794	X-RAY DIFFRACTION	99
1.75-1.78	0.3067	133	0.2676	2733	X-RAY DIFFRACTION	99
1.78-1.81	0.2601	177	0.2477	2695	X-RAY DIFFRACTION	100
1.81-1.85	0.2749	132	0.2449	2829	X-RAY DIFFRACTION	100
1.85-1.88	0.2868	156	0.2309	2743	X-RAY DIFFRACTION	100
1.88-1.92	0.2745	133	0.233	2775	X-RAY DIFFRACTION	100
1.92-1.96	0.2923	133	0.2134	2774	X-RAY DIFFRACTION	100
1.96-2.01	0.2173	151	0.193	2745	X-RAY DIFFRACTION	100
2.01-2.06	0.1997	142	0.173	2790	X-RAY DIFFRACTION	100
2.06-2.11	0.2104	140	0.1692	2794	X-RAY DIFFRACTION	100
2.11-2.17	0.1715	121	0.1597	2787	X-RAY DIFFRACTION	100
2.17-2.24	0.2116	163	0.1544	2769	X-RAY DIFFRACTION	100
2.24-2.32	0.1885	118	0.1559	2573	X-RAY DIFFRACTION	91
2.33-2.42	0.1558	102	0.1431	2809	X-RAY DIFFRACTION	100
2.42-2.53	0.1485	153	0.1433	2771	X-RAY DIFFRACTION	100
2.53-2.66	0.1846	168	0.1527	2641	X-RAY DIFFRACTION	99
2.68-2.83	0.1799	122	0.1492	2463	X-RAY DIFFRACTION	99
2.83-3.05	0.169	135	0.1509	2825	X-RAY DIFFRACTION	100
3.05-3.35	0.1688	134	0.1459	2819	X-RAY DIFFRACTION	100
3.35-3.84	0.1397	137	0.1358	2582	X-RAY DIFFRACTION	91
3.84-4.83	0.1142	141	0.1189	2848	X-RAY DIFFRACTION	100
4.83-38.79	0.1705	136	0.1661	2962	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	4.5765	2.9535	2.8929	3.1947	2.3836	2.5728	-0.003	0.2725	-0.4668	-0.1174	0.2626	-0.3696	0.0003	0.3129	-0.3289	0.1692	0.0388	0.031	0.2201	-0.037	0.2563	-11.8832	-47.6375	12.1972
2	5.0847	4.4196	2.8055	4.5515	3.0123	2.3207	0.0278	-0.1871	0.1783	0.1309	-0.1741	0.2767	0.0923	-0.0741	0.2617	0.1979	0.0423	0.0198	0.2419	-0.0173	0.2521	-18.5204	-43.4634	14.0449
3	4.3183	2.8757	0.4661	1.9309	0.1816	0.5468	-0.1704	0.3701	-1.106	-0.0094	0.1132	-0.6632	0.3328	0.4116	-0.145	0.2481	0.0412	0.0427	0.2563	-0.0602	0.3925	-15.9939	-57.846	10.4254
4	2.5991	0.1745	0.8135	0.3966	-0.0459	1.3736	0.0679	0.3863	-0.35	-0.0666	0.0831	-0.1765	0.2027	0.3489	-0.0868	0.194	0.0361	0.0336	0.2405	-0.0662	0.2869	-9.2137	-43.939	4.3992
5	2.9439	0.7769	0.3452	0.7856	0.1794	1.0587	-0.0135	0.3342	-0.0737	-0.0231	0.0685	-0.0027	0.0231	0.0877	-0.0156	0.1878	0.0113	0.0238	0.2241	-0.0496	0.2008	-16.9069	-38.143	3.2271
6	4.7332	1.8195	1.6246	1.4062	0.6998	1.187	0.0978	0.1364	-0.3062	0.0863	0.0246	-0.1938	0.2083	0.1802	-0.1102	0.2096	0.0588	0.0063	0.1763	0.0078	0.2326	-16.2838	-54.3289	25.4565
7	4.7936	3.4433	4.3606	3.2175	3.3077	5.1679	0.3668	0.0178	-0.9063	0.3468	0.1271	-0.5262	0.6545	0.2808	-0.5067	0.3088	0.0893	0.0222	0.2156	0.0383	0.3744	-16.3575	-61.7407	34.1416
8	9.4018	5.528	5.4591	3.7742	3.2307	4.478	0.1795	-0.3321	-0.3841	0.3631	-0.0523	-0.083	0.3433	-0.0181	-0.1039	0.2665	0.075	0.0029	0.1787	0.032	0.2791	-19.3421	-55.9223	38.368
9	2.6285	-2.1948	-0.0949	2.6952	-0.0442	0.6923	0.0008	0.0755	0.0595	-0.0198	0.0131	-0.1292	-0.1046	0.0685	-0.0125	0.1947	-0.0405	0.011	0.2192	-0.0174	0.1718	-19.3828	-8.0122	12.7776
10	1.1539	-0.3989	-0.1485	1.0093	0.5002	1.0158	0.0105	0.1012	0.1199	-0.0734	0.0672	-0.2221	-0.1517	0.1695	-0.0792	0.2149	-0.0683	0.0143	0.2331	-0.0063	0.2009	-13.3686	-2.7879	18.0706
11	2.7219	-1.5	-0.7836	1.6097	0.5459	0.7354	-0.005	0.1033	-0.0912	-0.0776	0.0102	-0.0226	-0.0763	0.0528	-0.0001	0.148	-0.026	-0.0026	0.1552	-0.0073	0.1032	-26.8529	-16.3789	2.7462
12	2.0101	-5.3348	9.4795	2.3439	-3.2531	10.0005	-0.0382	0.9321	0.607	-0.2638	-0.1619	-0.2085	-0.2328	0.5909	0.1173	0.2949	-0.0043	0.0439	0.3128	0.0476	0.2068	-20.7832	-9.6944	-3.2656
13	0.5855	-0.7063	-0.0234	2.6935	0.8634	0.5534	0.1033	0.2493	0.0552	-0.4688	-0.0563	-0.0745	-0.1947	-0.0355	-0.0214	0.2343	-0.0304	0.0124	0.2914	0.0185	0.1699	-33.2337	-16.755	-6.0328
14	7.3921	-6.154	-1.7243	6.6642	1.4271	1.1378	0.0304	0.3515	-0.2209	-0.1134	-0.0657	0.1665	-0.0025	-0.0664	0.0246	0.1595	-0.0314	0.0008	0.2288	-0.013	0.1258	-33.9187	-25.4993	-2.1442
15	2.0002	2	4.0478	2	-0.6848	1.1854	-0.3051	-0.1307	0.0104	0.2196	0.1116	0.0065	0.3165	0.1317	0.1819	0.8734	0.2739	-0.0561	0.7438	-0.2124	0.5649	-44.3997	-22.7354	-9.4023

Refinement TLS group

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

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