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- PDB-7vvv: Crystal structure of MmtN -

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Basic information

Entry
Database: PDB / ID: 7vvv
TitleCrystal structure of MmtN
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / methyltransferase / SAM dependent / trimer / rossmann-like
Function / homologymethyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / PHOSPHATE ION / SAM-dependent methyltransferase
Function and homology information
Biological speciesRoseovarius indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsPeng, M. / Li, C.Y.
Funding support China, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31630012 China
National Science Foundation (NSF, China)U1706207 China
National Science Foundation (NSF, China)91851205 China
National Science Foundation (NSF, China)42076229 China
National Science Foundation (NSF, China)31800107 China
National Science Foundation (NSF, China)41706152 China
National Science Foundation (NSF, China)42106142 China
CitationJournal: Nat Commun / Year: 2022
Title: Insights into methionine S-methylation in diverse organisms.
Authors: Peng, M. / Li, C.Y. / Chen, X.L. / Williams, B.T. / Li, K. / Gao, Y.N. / Wang, P. / Wang, N. / Gao, C. / Zhang, S. / Schoelmerich, M.C. / Banfield, J.F. / Miller, J.B. / Le Brun, N.E. / Todd, J.D. / Zhang, Y.Z.
History
DepositionNov 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8414
Polymers98,7463
Non-polymers951
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-18 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.734, 131.277, 134.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SAM-dependent methyltransferase


Mass: 32915.488 Da / Num. of mol.: 3 / Mutation: K141A/K143A/K146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius indicus (bacteria) / Gene: XM52_07085 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T5PCK9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.45→47.36 Å / Num. obs: 43546 / % possible obs: 98.64 % / Redundancy: 3.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Net I/σ(I): 16.8
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3945 / CC1/2: 0.927 / Rpim(I) all: 0.201 / Rrim(I) all: 0.499 / % possible all: 90.43

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→47.36 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 2253 5.18 %
Rwork0.1949 41245 -
obs0.1972 43498 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.92 Å2 / Biso mean: 57.102 Å2 / Biso min: 29.51 Å2
Refinement stepCycle: final / Resolution: 2.45→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 5 127 6304
Biso mean--46.02 48.69 -
Num. residues----811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.510.3171050.29512229233487
2.51-2.560.33691240.2782502262696
2.56-2.630.3021730.2612496266999
2.63-2.70.32971520.248325522704100
2.7-2.780.29411270.231526092736100
2.78-2.870.25241330.218625632696100
2.87-2.970.28371320.223525952727100
2.97-3.090.26911520.227925562708100
3.09-3.230.2341420.231826042746100
3.23-3.40.25141320.208326162748100
3.4-3.610.26211410.199826032744100
3.61-3.890.23871640.182325992763100
3.89-4.280.21041460.158226062752100
4.28-4.90.20651650.14726372802100
4.9-6.170.19011320.178726872819100
6.18-47.360.2151330.18132791292499

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