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- PDB-8ajp: Crystal structure of Halogen methyl transferase from Paraburkhold... -

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Basic information

Entry
Database: PDB / ID: 8ajp
TitleCrystal structure of Halogen methyl transferase from Paraburkholderia xenovorans at 1.8 A in complex with SAH
ComponentsHalide methyl transferase
KeywordsTRANSFERASE / Methyltransferase / SAH complex / Halide methyl transferase / SAM regeneration / biocatalysis / S-adenosylmethionine / late stage methylation
Function / homologyThiocyanate methyltransferase/thiol methyltransferase / Thiopurine S-methyltransferase (TPMT) / TPMT family / Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile. / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein
Function and homology information
Biological speciesParaburkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeisinger, F. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Synthetic Reagents for Enzyme-Catalyzed Methylation.
Authors: Wen, X. / Leisinger, F. / Leopold, V. / Seebeck, F.P.
History
DepositionJul 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: 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: Halide methyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2923
Polymers22,8721
Non-polymers4202
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.925, 90.814, 74.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Halide methyl transferase


Mass: 22871.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxe_A4046 / Production host: Escherichia coli (E. coli) / References: UniProt: Q145N6
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, Tris-HCl pH 8, CaCl2, LDAO.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.86 Å / Num. obs: 20584 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.048 / Rrim(I) all: 0.174 / Net I/σ(I): 11.1 / Num. measured all: 273648 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8412.71.1411525912020.9280.3311.1892.5100
9-42.8610.90.09421742000.9990.030.09926.599.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LCC

3lcc


Resolution: 1.8→42.86 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1015 4.94 %
Rwork0.1807 19528 -
obs0.1816 20543 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.95 Å2 / Biso mean: 23.8001 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: final / Resolution: 1.8→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 46 123 1731
Biso mean--20.97 28.71 -
Num. residues----199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.890.31561290.235127632892
1.89-2.010.25691480.213527302878
2.01-2.170.24051470.1927632910
2.17-2.390.19871420.184327752917
2.39-2.730.24841540.181327662920
2.73-3.440.1851350.188428252960
3.44-42.860.15541600.15729063066

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