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

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Basic information

Entry
Database: PDB / ID: 9qqh
TitleMini-bacterioferritin from Candidatus Methanoperedens species BLZ2 oxidized then chemically reduced
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / ferritin-like protein / mini-ferritin / Fe-coproporphyrin III / anaerobic methane-oxidising archaea / archaea / iron homeostasis / iron storage / dodecamer / nano-compartment / chemical reduction
Function / homology: / Chem-FEC
Function and homology information
Biological speciesCandidatus Methanoperedens sp. BLZ2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWissink, M. / Wagner, T.
Funding supportEuropean Union, Germany, Netherlands, 6items
OrganizationGrant numberCountry
European Research Council (ERC)101125699European 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)854088European Union
CitationJournal: 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
DepositionMar 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,79615
Polymers63,8764
Non-polymers1,92011
Water9,728540
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


Theoretical massNumber of molelcules
Total (without water)197,38845
Polymers191,62912
Non-polymers5,75933
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)122.897, 122.897, 122.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-386-

HOH

21D-443-

HOH

31D-447-

HOH

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Components

#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.: 9 / Source method: isolated from a natural source / 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.: 2 / Source method: obtained synthetically / Formula: C36H36FeN4O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 %
Description: Triangular pink plate becoming brownish upon oxidation and switching back to pink upon dithionite addition
Crystal growTemperature: 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 exposed to air for 10 min, then soaked in the crystallization solution supplemented with 100 mM of freshly prepared sodium dithionite. Finally the crystal was soaked in the crystallization solution supplemented with 20% v/v glycerol and 90 mM sodium dithionite prior freezing.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: / / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.078→86.901 Å / Num. obs: 37379 / % possible obs: 99.7 % / Redundancy: 7.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.064 / Rrim(I) all: 0.186 / Net I/σ(I): 7.1
Reflection shellResolution: 2.078→2.114 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1806 / CC1/2: 0.374 / Rpim(I) all: 0.925 / Rrim(I) all: 1.601 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→86.9 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.63 / 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 ...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 validated by the molprobity tool integrated with PHENIX and with the Molprobity online server.
RfactorNum. reflection% reflection
Rfree0.2295 1781 4.91 %
Rwork0.1955 --
obs0.1971 36283 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.37 Å2
Refinement stepCycle: LAST / Resolution: 2.08→86.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4415 0 107 540 5062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064838
X-RAY DIFFRACTIONf_angle_d0.8226587
X-RAY DIFFRACTIONf_dihedral_angle_d15.9891934
X-RAY DIFFRACTIONf_chiral_restr0.048681
X-RAY DIFFRACTIONf_plane_restr0.008836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.32691510.27992428X-RAY DIFFRACTION91
2.13-2.20.28021460.25122663X-RAY DIFFRACTION98
2.2-2.270.3764910.33362026X-RAY DIFFRACTION75
2.27-2.350.31481210.24672658X-RAY DIFFRACTION97
2.35-2.440.23941500.21762679X-RAY DIFFRACTION100
2.44-2.550.23091380.21392714X-RAY DIFFRACTION100
2.55-2.690.25461240.22742748X-RAY DIFFRACTION100
2.69-2.860.28511330.22822739X-RAY DIFFRACTION100
2.86-3.080.24411420.19782728X-RAY DIFFRACTION100
3.08-3.390.21071620.19382714X-RAY DIFFRACTION100
3.39-3.880.22561500.17332744X-RAY DIFFRACTION99
3.88-4.880.1611450.13212773X-RAY DIFFRACTION100
4.89-86.90.18821280.17072888X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
12.9569-2.9817-2.17024.34742.48472.0160.02290.03940.0123-0.0555-0.0121-0.0839-0.0686-0.0178-0.00390.1976-0.03470.00950.20730.02330.225715.627314.9619-18.0131
20.2198-0.19620.3361.91560.81051.2137-0.01520.1450.161-0.29750.0578-0.2287-0.25240.1453-0.09940.2728-0.05280.07950.26290.06220.324514.86320.7684-25.7907
31.6206-2.7804-0.09196.96361.25430.61170.08980.13560.1034-0.1201-0.0677-0.11060.042-0.0356-0.02020.2553-0.0530.03550.21670.03550.187.364613.4484-27.6267
41.356-1.7041-0.86435.96722.35451.64050.01670.01890.09860.05860.0765-0.2023-0.05030.1858-0.09960.1496-0.01710.00140.20050.01470.174822.581614.9241-4.7661
52.348-2.2258-2.50362.25082.7754.28280.0101-0.03680.208-0.21140.2091-0.3778-0.28570.5099-0.32770.2024-0.07580.01740.30420.0080.302631.36112.90251.1363
63.2116-3.9575-2.99117.21524.18393.86270.1355-0.07860.19590.1672-0.0947-0.47120.03570.0987-0.01530.1682-0.0157-0.04220.22280.02430.221725.010811.06277.5736
72.52121.66630.34131.7649-0.11011.0454-0.2002-0.06660.2611-0.23430.07410.1555-0.098-0.11480.14270.22720.0675-0.0150.2220.01550.1752-23.452213.8723-20.4559
84.19173.80470.59384.14040.76520.43590.4494-0.2411-0.17160.4153-0.3844-0.20770.04-0.0971-0.04460.24450.0321-0.00380.20920.02430.1435-20.83488.6105-14.8143
91.47861.98640.23864.649-0.0530.31870.16120.24480.12860.004-0.09990.11010.04390.0221-0.03750.30960.09180.00690.25590.04040.2252-25.947613.0292-25.8774
103.89272.7756-2.82533.0692-2.01122.72340.02160.43420.2223-0.25910.210.2103-0.085-0.4049-0.29140.25360.0832-0.02540.26780.0390.2538-29.761419.2851-14.085
114.22974.4493-1.31185.9464-1.29541.0153-0.1046-0.0162-0.0509-0.0570.0819-0.12470.0588-0.01960.04980.1660.05050.00470.20420.02140.1676-27.290215.0353-7.4607
121.79651.2575-0.35672.0985-0.65570.7993-0.03240.12230.0403-0.14350.02240.0195-0.0022-0.0801-0.00090.23560.0362-0.00750.22530.00550.174-14.64263.571-28.1115
132.56380.8926-0.53081.00770.09170.416-0.0740.4958-0.116-0.2640.1460.12410.0674-0.2935-0.06250.29960.0389-0.05130.2548-0.00010.1591-14.1678-2.6313-36.8284
146.15925.3728-0.86326.6256-1.00710.2587-0.13490.3533-0.1456-0.29440.1665-0.21980.07620.0473-0.04330.27530.03290.03050.24750.00790.1325-5.5148-4.0283-33.3325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 139 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 73 )
5X-RAY DIFFRACTION5chain 'B' and (resid 74 through 107 )
6X-RAY DIFFRACTION6chain 'B' and (resid 108 through 139 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 34 )
8X-RAY DIFFRACTION8chain 'C' and (resid 35 through 63 )
9X-RAY DIFFRACTION9chain 'C' and (resid 64 through 79 )
10X-RAY DIFFRACTION10chain 'C' and (resid 80 through 107 )
11X-RAY DIFFRACTION11chain 'C' and (resid 108 through 137 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 72 )
13X-RAY DIFFRACTION13chain 'D' and (resid 73 through 107 )
14X-RAY DIFFRACTION14chain 'D' and (resid 108 through 139 )

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