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- PDB-6fns: Ergothioneine-biosynthetic methyltransferase EgtD in complex with... -

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Basic information

Entry
Database: PDB / ID: 6fns
TitleErgothioneine-biosynthetic methyltransferase EgtD in complex with morpholinohistidine
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / ergothioneine / methyltransferase / inhibitor complex
Function / homology
Function and homology information


: / ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / L-histidine N(alpha)-methyltransferase activity / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide / protein methyltransferase activity / methylation
Similarity search - Function
Methyltransferase EgtD-like / Histidine-specific methyltransferase, SAM-dependent / Histidine N-alpha-methyltransferase, Actinobacteria-type / Histidine N-alpha-methyltransferase / : / Histidine-specific methyltransferase, SAM-dependent / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Morpholinohistidine / Histidine N-alpha-methyltransferase / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsVit, A. / Blankenfeldt, W. / Seebeck, F.P.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Inhibition and Regulation of the Ergothioneine Biosynthetic Methyltransferase EgtD.
Authors: Misson, L. / Burn, R. / Vit, A. / Hildesheim, J. / Beliaeva, M.A. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionFeb 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine N-alpha-methyltransferase
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2046
Polymers70,5652
Non-polymers6394
Water8,629479
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6023
Polymers35,2831
Non-polymers3192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6023
Polymers35,2831
Non-polymers3192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.689, 76.153, 138.662
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 Histidine N-alpha-methyltransferase / Histidine trimethyltransferase


Mass: 35282.695 Da / Num. of mol.: 2 / Fragment: EgtD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: egtD, ERS451418_06055 / Plasmid: pET19m / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0D6J225, UniProt: A0R5M8*PLUS, L-histidine Nalpha-methyltransferase
#2: Chemical ChemComp-DY8 / Morpholinohistidine


Mass: 227.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% (w/v) PEG 8000, 20% (v/v) glycerol, 0.16 M Mg-Acetate, 0.08 M Na-Cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2014
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→48.85 Å / Num. obs: 65608 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 24.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 18 / Num. measured all: 862107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.8911.51.40440030.6880.4271.469100
9.06-48.8510.50.02665610.0080.02799.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PIM

4pim


Resolution: 1.85→41.701 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.01 / Details: FOURIER SYNTHESIS
RfactorNum. reflection% reflection
Rfree0.184 3294 5.03 %
Rwork0.1632 --
obs0.1643 65524 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.95 Å2 / Biso mean: 31.4694 Å2 / Biso min: 0.02 Å2
Refinement stepCycle: final / Resolution: 1.85→41.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4914 0 89 479 5482
Biso mean--39.48 37.11 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045067
X-RAY DIFFRACTIONf_angle_d0.936893
X-RAY DIFFRACTIONf_chiral_restr0.035794
X-RAY DIFFRACTIONf_plane_restr0.004903
X-RAY DIFFRACTIONf_dihedral_angle_d13.2451817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.87650.25411350.253425512686
1.8765-1.90450.22551290.243925902719
1.9045-1.93420.26821210.220725712692
1.9342-1.9660.27981290.210125292658
1.966-1.99990.24651350.19326002735
1.9999-2.03620.22211440.191525162660
2.0362-2.07540.2091210.181725862707
2.0754-2.11770.20561420.17425842726
2.1177-2.16380.21560.169725342690
2.1638-2.21410.18661110.169925782689
2.2141-2.26950.19891390.154225732712
2.2695-2.33080.18461510.161925592710
2.3308-2.39940.19341460.156625842730
2.3994-2.47690.16411230.165326052728
2.4769-2.56540.15971580.164425552713
2.5654-2.66810.19381510.164425642715
2.6681-2.78950.17851310.170125822713
2.7895-2.93650.21431430.172825982741
2.9365-3.12040.20281360.163826182754
3.1204-3.36130.16111360.159326012737
3.3613-3.69930.18481230.140926462769
3.6993-4.23420.1651490.134126442793
4.2342-5.33290.13481330.135926672800
5.3329-41.71150.18541520.181927952947
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)
10.5440.4003-0.19720.6378-0.09490.65780.0641-0.04940.0154-0.0002-0.06260.0167-0.02340.0364-0.01090.18250.0074-0.02140.20090.02730.216812.286717.534420.4408
23.0362-0.4002-1.27651.83880.3363.2320.0487-0.0522-0.3931-0.1204-0.19580.01630.17860.42110.1110.29870.0109-0.02030.30670.03340.238121.009828.238215.3727
31.3828-0.1709-0.29130.5915-0.04741.5960.0628-0.0035-0.02220.02160.0136-0.03320.09040.2362-0.0650.2657-0.0396-0.02160.3056-0.00650.212823.245430.007921.0408
40.5130.2313-0.15831.0184-0.42670.73240.03070.0030.0178-0.03930.02580.1635-0.0587-0.1167-0.04840.18710.0094-0.02150.22170.01670.19594.291516.998216.7821
52.1080.8659-0.19910.7543-0.0530.7808-0.1260.2165-0.1965-0.16570.06690.05970.11580.03350.04110.2749-0.0169-0.02760.21840.02760.283530.6066-8.66244.8629
61.6644-0.00510.08880.2080.0770.4361-0.1395-0.29220.24180.03420.05450.0654-0.0887-0.07340.07210.21710.0136-0.02940.24330.01670.250134.31841.663626.121
71.1934-0.48710.26960.9384-0.48212.0831-0.09550.00980.09430.0220.1280.08-0.1653-0.2261-0.02220.2421-0.0045-0.00430.24690.04880.219745.26154.554513.7569
81.2194-0.16660.36650.2595-0.0840.7940.0229-0.1154-0.2373-0.04840.03320.07210.1814-0.0684-0.05750.2451-0.0084-0.02540.18780.0350.250630.6096-11.623419.5471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 77 )A0 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 95 )A78 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 145 )A96 - 145
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 321 )A146 - 321
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 40 )B-1 - 40
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 77 )B41 - 77
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 145 )B78 - 145
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 321 )B146 - 321

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