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- PDB-9nzy: Structure of Methanogen MtxX (Methanogen Marker Protein MMP4) fro... -

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Basic information

Entry
Database: PDB / ID: 9nzy
TitleStructure of Methanogen MtxX (Methanogen Marker Protein MMP4) from Methanothermobacter thermautotrophicus
ComponentsUncharacterized methyltransferase MTH_231
KeywordsUNKNOWN FUNCTION / MtxX / MMP4 / Methanogen / Archaea / Methanothermobacter thermautotrophicus
Function / homologyMethyltransferase Mtx, subunit X / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / Uncharacterized methyltransferase MTH_231
Function and homology information
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsSutherland-Smith, A.J. / Carbone, V. / Schofield, L.R. / Ronimus, R.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other government New Zealand
CitationJournal: Fems Microbes / Year: 2026
Title: Crystal structure of methanogen MtxX (Methanogen Marker Protein MMP4) from Methanothermobacter thermautotrophicus Delta H.
Authors: Sutherland-Smith, A.J. / Carbone, V. / Kaziur-Cegla, W. / Woermann, M. / Schofield, L.R. / Ronimus, R.S.
History
DepositionApr 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized methyltransferase MTH_231
B: Uncharacterized methyltransferase MTH_231
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4503
Polymers60,3882
Non-polymers621
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-18 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.484, 72.31, 65.58
Angle α, β, γ (deg.)90, 96.115, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized methyltransferase MTH_231


Mass: 30194.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: MTH_231 / Plasmid: pET151D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): K12
References: UniProt: O26333, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.21 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na HEPES pH 7.5, 10% w/v PEG 8000, 8% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953653 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2017 / Details: Si mirrors with Rh stripes
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953653 Å / Relative weight: 1
ReflectionResolution: 1.6→65.29 Å / Num. obs: 69258 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 1 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 15.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3397 / CC1/2: 0.78 / Rpim(I) all: 0.48 / Rrim(I) all: 1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→65.29 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.873 / SU ML: 0.061 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.185 3507 5.065 %Random selection
Rwork0.1628 65729 --
all0.164 ---
obs-69236 99.951 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.313 Å2-0 Å20.84 Å2
2---0.612 Å20 Å2
3---0.728 Å2
Refinement stepCycle: LAST / Resolution: 1.6→65.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 4 282 3851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123665
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163525
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.8264950
X-RAY DIFFRACTIONr_angle_other_deg0.6051.7648060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.829545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8110618
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.13210177
X-RAY DIFFRACTIONr_chiral_restr0.090.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_nbd_refined0.2230.2689
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.23031
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21835
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2245
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.26
X-RAY DIFFRACTIONr_nbd_other0.1420.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.216
X-RAY DIFFRACTIONr_mcbond_it2.6652.4851866
X-RAY DIFFRACTIONr_mcbond_other2.6642.4871867
X-RAY DIFFRACTIONr_mcangle_it3.8754.4472332
X-RAY DIFFRACTIONr_mcangle_other3.8754.452333
X-RAY DIFFRACTIONr_scbond_it4.2023.0721799
X-RAY DIFFRACTIONr_scbond_other4.2013.0721800
X-RAY DIFFRACTIONr_scangle_it6.495.3612612
X-RAY DIFFRACTIONr_scangle_other6.4895.3612613
X-RAY DIFFRACTIONr_lrange_it8.4726.2984120
X-RAY DIFFRACTIONr_lrange_other8.43525.0564040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6410.2942810.3164785X-RAY DIFFRACTION99.5285
1.641-1.6860.3062650.2974702X-RAY DIFFRACTION100
1.686-1.7350.2572080.2564621X-RAY DIFFRACTION100
1.735-1.7880.2372510.224427X-RAY DIFFRACTION100
1.788-1.8470.2072310.1964337X-RAY DIFFRACTION100
1.847-1.9120.1972150.1724194X-RAY DIFFRACTION100
1.912-1.9840.2061970.1684056X-RAY DIFFRACTION100
1.984-2.0650.1942180.1623875X-RAY DIFFRACTION100
2.065-2.1560.171990.1483730X-RAY DIFFRACTION100
2.156-2.2610.1752020.153571X-RAY DIFFRACTION100
2.261-2.3840.1611680.1343380X-RAY DIFFRACTION100
2.384-2.5280.1481660.1353240X-RAY DIFFRACTION100
2.528-2.7020.1861810.1473012X-RAY DIFFRACTION100
2.702-2.9180.1791450.1512816X-RAY DIFFRACTION100
2.918-3.1960.2071430.1592586X-RAY DIFFRACTION100
3.196-3.5720.171260.1612358X-RAY DIFFRACTION100
3.572-4.1230.1561010.1472094X-RAY DIFFRACTION100
4.123-5.0450.184840.1381787X-RAY DIFFRACTION100
5.045-7.1130.185810.1751374X-RAY DIFFRACTION100
7.113-65.290.155450.165784X-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)
10.4828-0.05630.00520.37070.02310.0036-0.01160.0018-0.02980.00190.002-0.04460.0008-0.00540.00960.00260.00040.0010.0485-0.00210.157142.52742.191239.5678
20.1311-0.1921-0.27711.09340.03120.7823-0.02230.0132-0.01220.26090.03860.129-0.0724-0.0306-0.01630.08340.01330.02730.0378-0.00050.141726.04723.457556.212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp7 - 242
2X-RAY DIFFRACTION2ALLBp8 - 235

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