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Entry
Database: PDB / ID: 8cns
TitleThe Hybrid Cluster Protein from the thermophilic methanogen Methanothermococcus thermolithotrophicus in a mixed redox state after soaking with hydroxylamine, at 1.36-A resolution.
ComponentsHybrid cluster protein from Methanothermococcus thermolithotrophicus
KeywordsOXIDOREDUCTASE / Hybrid cluster / prismane protein / Hybrid cluster protein / methanogenic archaea / anaerobic biochemistry / thermophile / metallocluster / Nitric oxide reductase / hydroxylamine
Function / homologyACETATE ION / FORMIC ACID / HYDROXYAMINE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / :
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLemaire, O.N. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)Schwerpunktprogram 1927 Iron-sulfur for Life WA 4053/1-1 Germany
CitationJournal: Front Microbiol / Year: 2023
Title: Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon.
Authors: Lemaire, O.N. / Belhamri, M. / Wagner, T.
History
DepositionFeb 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Sep 2, 2026Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hybrid cluster protein from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,46538
Polymers60,3361
Non-polymers3,12937
Water11,331629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-9 kcal/mol
Surface area20250 Å2
Unit cell
Length a, b, c (Å)97.773, 102.186, 58.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1363-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hybrid cluster protein from Methanothermococcus thermolithotrophicus


Mass: 60335.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Compared to the automatic annotation, the sequence has a five-residue extension in its N-terminal (MRPSK). The cysteine 402 has a thiol addition in its oxidized state.
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: hydroxylamine reductase

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Non-polymers , 14 types, 666 molecules

#2: Chemical
ChemComp-HOA / HYDROXYAMINE


Mass: 33.030 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H3NO
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#12: Chemical ChemComp-VFQ / hybrid cluster with four iron three oxygen and three sulfur


Mass: 367.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O3S3 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#14: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Description: Brown orthorhombic rod. Appeared after few weeks.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Crystallisation was performed anaerobically by initial screening at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a ...Details: Crystallisation was performed anaerobically by initial screening at 20 degree Celsius using the sitting drop method on 96-Well MRC 2-Drop polystyrene Crystallisation Plates (SWISSCI) in a Coy tent containing a N2/H2 (97:3%) atmosphere. The reservoir chamber was filled with 90 ul of crystallisation condition, and the crystallisation drop was formed by spotting 0.55 ul protein with 0.55 ul of 20% (w/v) PEG 3,350 and 200 mM Magnesium formate. The protein was crystallised at 9.9 mg/ml in 25 mM Tris/HCl pH 7.6, 2 mM dithiothreitol, 10% (v/v) glycerol. Densities in the electron density map suggest a contamination of another crystallisation condition spatially close and containing 30% (v/v) 2-Methyl-2,4-pentanediol, 20 mM Calcium chloride and 100 mM Sodium acetate, pH 4.6. The crystal was soaked for 5.7 min in a solution of 100 mM hydroxylamine/HCl in the crystallisation condition and then soaked in the crystallisation solution supplemented with 20% v/v ethylene glycol for a few seconds before freezing in liquid nitrogen.
PH range: / / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0004 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.356→70.645 Å / Num. obs: 89372 / % possible obs: 94.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.043 / Rrim(I) all: 0.118 / Net I/σ(I): 11.5
Reflection shellResolution: 1.356→1.476 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4469 / CC1/2: 0.611 / Rpim(I) all: 0.472 / Rrim(I) all: 1.165 / % possible all: 67.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→51.09 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.74 / Stereochemistry target values: ML
Details: Refinement steps were performed by considering all atoms anisotropic. The model was refined with hydrogens in riding position. Hydrogens were omitted in the final deposited model.
RfactorNum. reflection% reflection
Rfree0.1661 4367 4.89 %
Rwork0.129 --
obs0.1309 89365 70.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.44 Å2
Refinement stepCycle: LAST / Resolution: 1.36→51.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 160 629 5025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124624
X-RAY DIFFRACTIONf_angle_d1.3526250
X-RAY DIFFRACTIONf_dihedral_angle_d14.4131717
X-RAY DIFFRACTIONf_chiral_restr0.098706
X-RAY DIFFRACTIONf_plane_restr0.011803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.370.130440.255680X-RAY DIFFRACTION2
1.37-1.390.218180.2208195X-RAY DIFFRACTION5
1.39-1.40.177130.2113350X-RAY DIFFRACTION9
1.4-1.420.3011210.1965546X-RAY DIFFRACTION13
1.42-1.440.2732410.2104835X-RAY DIFFRACTION21
1.44-1.460.2012610.20691168X-RAY DIFFRACTION29
1.46-1.480.2408740.19751496X-RAY DIFFRACTION38
1.48-1.50.2425940.20021713X-RAY DIFFRACTION43
1.5-1.530.2412920.19131886X-RAY DIFFRACTION47
1.53-1.550.211040.19542091X-RAY DIFFRACTION52
1.55-1.580.22841060.17682275X-RAY DIFFRACTION57
1.58-1.610.23631440.17562509X-RAY DIFFRACTION63
1.61-1.640.2411280.17332824X-RAY DIFFRACTION71
1.64-1.670.20311560.17133100X-RAY DIFFRACTION77
1.67-1.710.21731520.15813366X-RAY DIFFRACTION84
1.71-1.750.21271940.15293733X-RAY DIFFRACTION93
1.75-1.790.24171810.14053947X-RAY DIFFRACTION98
1.79-1.840.19411990.13374048X-RAY DIFFRACTION100
1.84-1.890.18212170.12923994X-RAY DIFFRACTION100
1.89-1.960.1582210.11954013X-RAY DIFFRACTION100
1.96-2.030.16152060.11364017X-RAY DIFFRACTION100
2.03-2.110.15582410.10633998X-RAY DIFFRACTION100
2.11-2.20.15532060.10224020X-RAY DIFFRACTION100
2.2-2.320.15352040.09814086X-RAY DIFFRACTION100
2.32-2.460.14441970.10334033X-RAY DIFFRACTION100
2.46-2.650.13661950.10814109X-RAY DIFFRACTION100
2.65-2.920.15282140.11474069X-RAY DIFFRACTION100
2.92-3.340.1592200.11744070X-RAY DIFFRACTION100
3.34-4.210.132520.1114117X-RAY DIFFRACTION100
4.21-51.090.16872320.16554310X-RAY DIFFRACTION100

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