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- PDB-7xcm: Crystal structure of sulfite MttB structure at 3.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 7xcm
TitleCrystal structure of sulfite MttB structure at 3.2 A resolution
ComponentsTrimethylamine methyltransferaseTrimethylamine-corrinoid protein Co-methyltransferase
KeywordsTRANSFERASE / pyrrolysine / trimethylamine / methyltransferase / corrinoid protein
Function / homology
Function and homology information


trimethylamine-corrinoid protein Co-methyltransferase / trimethylamine methyltransferase activity / methanogenesis / methylation
Similarity search - Function
Trimethylamine methyltransferase, Methanosarcina / Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB)
Similarity search - Domain/homology
3-METHYL-5-SULFO-PYRROLIDINE-2-CARBOXYLIC ACID / Trimethylamine methyltransferase
Similarity search - Component
Biological speciesMethanosarcina barkeri MS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, J. / Chan, M.K.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14116620 Hong Kong
CitationJournal: Commun Biol / Year: 2023
Title: Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex.
Authors: Li, J. / Kang, P.T. / Jiang, R. / Lee, J.Y. / Soares, J.A. / Krzycki, J.A. / Chan, M.K.
History
DepositionMar 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimethylamine methyltransferase
B: Trimethylamine methyltransferase
C: Trimethylamine methyltransferase
D: Trimethylamine methyltransferase
E: Trimethylamine methyltransferase
F: Trimethylamine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,88529
Polymers328,4786
Non-polymers2,40623
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50220 Å2
ΔGint-317 kcal/mol
Surface area88030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.840, 174.840, 300.121
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Trimethylamine methyltransferase / Trimethylamine-corrinoid protein Co-methyltransferase


Mass: 54746.387 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri MS (archaea) / Gene: MSBRM_0461 / Production host: Methanosarcina acetivorans C2A (archaea)
References: UniProt: A0A0E3QRM4, trimethylamine-corrinoid protein Co-methyltransferase
#2: Chemical
ChemComp-BG3 / 3-METHYL-5-SULFO-PYRROLIDINE-2-CARBOXYLIC ACID


Mass: 209.220 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H11NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.11 Å3/Da / Density % sol: 70.1 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 1 ul protein (8 mg/mL MttB in 20 mM potassium phosphate buffer pH 7.4, 500 mM NaCl, 240 mM imidazole, 20% glycerol), 1 ul reservoir (4% MPD, 0.1 M citric acid pH 4.5) solutions, reservoir ...Details: 1 ul protein (8 mg/mL MttB in 20 mM potassium phosphate buffer pH 7.4, 500 mM NaCl, 240 mM imidazole, 20% glycerol), 1 ul reservoir (4% MPD, 0.1 M citric acid pH 4.5) solutions, reservoir solution containing saturated sodium dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 74099 / % possible obs: 85.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 2.6
Reflection shellResolution: 3.2→3.27 Å / Num. unique obs: 11486 / Rpim(I) all: 0.254

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Processing

Software
NameVersionClassification
CNSrefinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7xcl

7xcl


Resolution: 3.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.243 7479 8.5 %
Rwork0.1665 66605 -
obs-74084 84.5 %
Solvent computationBsol: 46.955 Å2
Displacement parametersBiso max: 149.96 Å2 / Biso mean: 53.0752 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--10.096 Å20 Å20 Å2
2---10.096 Å20 Å2
3---20.192 Å2
Refinement stepCycle: final / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22588 0 144 165 22897
Biso mean--67.91 28.77 -
Num. residues----2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.277
X-RAY DIFFRACTIONc_mcbond_it7.0241.5
X-RAY DIFFRACTIONc_scbond_it11.4432
X-RAY DIFFRACTIONc_mcangle_it10.1642
X-RAY DIFFRACTIONc_scangle_it14.2072.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.310.33897870.24797002778990.2
3.31-3.450.32597950.23467019781489.9
3.45-3.60.3087790.22146957773689.3
3.6-3.790.27427480.19856981772988.7
3.79-4.030.26447620.17826776753886.5
4.03-4.330.23677690.15116456722582.8
4.33-4.770.20197300.13226314704480.4
4.77-5.440.20376490.12836295694478.9
5.44-6.810.2387100.16146184689477.9
6.81-200.17257500.12076621737181
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6x7so3.param
X-RAY DIFFRACTION7na6.param
X-RAY DIFFRACTION8gol.param
X-RAY DIFFRACTION9cis_peptide_40pro111thr223pro.param

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