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- PDB-9qq4: Mini-bacterioferritin from Candidatus Methanoperedens species BLZ... -

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Basic information

Entry
Database: PDB / ID: 9qq4
TitleMini-bacterioferritin from Candidatus Methanoperedens species BLZ2 as isolated form at 1.07-A resolution
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / 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 speciesCandidatus Methanoperedens sp. BLZ2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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)67,93533
Polymers63,8764
Non-polymers4,05929
Water16,646924
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)203,80699
Polymers191,62912
Non-polymers12,17687
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area59980 Å2
ΔGint-957 kcal/mol
Surface area53350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.608, 87.608, 131.374
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-493-

HOH

21A-546-

HOH

31D-484-

HOH

41D-507-

HOH

51D-517-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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: /

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Non-polymers , 7 types, 953 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.31 Å3/Da / Density % sol: 46.83 % / Description: Light pink bipyramids
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The crystal was obtained from an initial screening using the sitting drop method performed on a 96-well MRC 2-well polystyrene crystallisation plate (SWISSCI, Switzerland) at 20 degree ...Details: The crystal was obtained from an initial screening using the sitting drop method performed on a 96-well MRC 2-well polystyrene crystallisation plate (SWISSCI, Switzerland) at 20 degree Celsius under a pure N2 atmosphere. The plate was filled with 90 uL crystallisation solution in the large reservoir and the purified protein solution concentrated to 4.4 mg/mL was spotted in the small reservoirs by mixing 0.5 uL purified protein with 0.5 uL crystallisation solution using an OryxNano robot (Douglas Instruments Ltd, UK). The crystallisation solution was composed of: 20 % v/v Jeffamine M-600 pH 7.0, and 100 mM HEPES pH 7.5. Once prepared, the plate was transferred to an anaerobic chamber containing an N2/H2 (97/3 percent) atmosphere for long-term storage. Prior liquid nitrogen freezing, the crystal was soaked in the crystallization solution supplemented with 25 % v/v glycerol for a few seconds.
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: / / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.067→75.871 Å / Num. obs: 221484 / % possible obs: 95.8 % / Redundancy: 15.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.02 / Rrim(I) all: 0.084 / Net I/σ(I): 18.5
Reflection shellResolution: 1.067→1.129 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11074 / CC1/2: 0.654 / Rpim(I) all: 0.466 / Rrim(I) all: 1.154 / % possible all: 58.4

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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: 1.07→75.87 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.64 / Stereochemistry target values: ML
Details: The model was manually optimised with Coot (v0.9.8). Refinement was performed with Phenix refine (v1.21.1-5286) (Liebschner et al., 2019) without applying non-crystallography symmetry. The ...Details: The model was manually optimised with Coot (v0.9.8). Refinement was performed with Phenix refine (v1.21.1-5286) (Liebschner et al., 2019) without applying non-crystallography symmetry. The model was refined by considering all atoms anisotropic with hydrogens in riding positions. The model was validated by the molprobity tool integrated with PHENIX (Emsley et al., 2010; Liebschner et al., 2019) and with the oline MolProbity server (http://molprobity.biochem.duke.edu).
RfactorNum. reflection% reflection
Rfree0.1254 11147 5.03 %
Rwork0.1078 --
obs0.1087 221476 87.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.31 Å2
Refinement stepCycle: LAST / Resolution: 1.07→75.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 250 924 5597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015185
X-RAY DIFFRACTIONf_angle_d1.2677072
X-RAY DIFFRACTIONf_dihedral_angle_d15.1482088
X-RAY DIFFRACTIONf_chiral_restr0.083712
X-RAY DIFFRACTIONf_plane_restr0.013925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.080.3088340.2724479X-RAY DIFFRACTION6
1.08-1.090.3263530.23851061X-RAY DIFFRACTION13
1.09-1.110.23451090.22311972X-RAY DIFFRACTION25
1.11-1.120.23741860.2183569X-RAY DIFFRACTION45
1.12-1.130.2422910.20435483X-RAY DIFFRACTION69
1.13-1.150.22224020.18146720X-RAY DIFFRACTION86
1.15-1.170.2193400.15927701X-RAY DIFFRACTION96
1.17-1.180.15964150.14127883X-RAY DIFFRACTION98
1.18-1.20.15894350.12617758X-RAY DIFFRACTION99
1.2-1.220.13114250.11547933X-RAY DIFFRACTION99
1.22-1.240.14113800.10967978X-RAY DIFFRACTION100
1.24-1.270.13324810.11217924X-RAY DIFFRACTION100
1.27-1.290.12884310.10997970X-RAY DIFFRACTION100
1.29-1.320.1394320.11277954X-RAY DIFFRACTION100
1.32-1.340.12943850.10268033X-RAY DIFFRACTION100
1.34-1.380.10784630.09277898X-RAY DIFFRACTION100
1.38-1.410.1153810.09358037X-RAY DIFFRACTION100
1.41-1.450.11213820.08958017X-RAY DIFFRACTION100
1.45-1.490.09174130.08337980X-RAY DIFFRACTION100
1.49-1.540.09683790.07978022X-RAY DIFFRACTION100
1.54-1.590.10764510.08347955X-RAY DIFFRACTION100
1.59-1.660.10994040.08848001X-RAY DIFFRACTION100
1.66-1.730.1034130.09047978X-RAY DIFFRACTION100
1.73-1.830.10414610.09067999X-RAY DIFFRACTION100
1.83-1.940.1114550.09587911X-RAY DIFFRACTION100
1.94-2.090.10264050.09348020X-RAY DIFFRACTION100
2.09-2.30.11264230.09638011X-RAY DIFFRACTION100
2.3-2.630.11984480.10267997X-RAY DIFFRACTION100
2.63-3.320.12954490.11457982X-RAY DIFFRACTION100
3.32-75.870.14064210.12898103X-RAY DIFFRACTION100

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