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

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Basic information

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


: / ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / : / 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
Pyrrolidinohistidine / Histidine N-alpha-methyltransferase / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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)70,9884
Polymers70,5652
Non-polymers4232
Water5,567309
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4942
Polymers35,2831
Non-polymers2111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4942
Polymers35,2831
Non-polymers2111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.768, 77.535, 139.045
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-AVO / Pyrrolidinohistidine


Mass: 211.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
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: 1.9→49.25 Å / Num. obs: 61947 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.089 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.9413.81.38239550.8250.3821.434100
9.11-49.2510.50.036560.9990.0090.03199.2

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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: 1.9→41.982 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.01 / Details: FOURIER SYNTHESIS
RfactorNum. reflection% reflection
Rfree0.2071 3107 5.02 %
Rwork0.1701 --
obs0.172 61858 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 244.52 Å2 / Biso mean: 44.6038 Å2 / Biso min: 22.22 Å2
Refinement stepCycle: final / Resolution: 1.9→41.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 60 309 5288
Biso mean--42.51 45.12 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045080
X-RAY DIFFRACTIONf_angle_d0.8766917
X-RAY DIFFRACTIONf_chiral_restr0.033797
X-RAY DIFFRACTIONf_plane_restr0.004909
X-RAY DIFFRACTIONf_dihedral_angle_d13.1341830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.92970.37031180.28926542772
1.9297-1.96130.3121340.260926412775
1.9613-1.99520.29371420.24626402782
1.9952-2.03140.27671390.221926092748
2.0314-2.07050.26441370.209226302767
2.0705-2.11280.20921250.1926762801
2.1128-2.15870.2291690.188326302799
2.1587-2.20890.21081340.186226262760
2.2089-2.26420.23771220.177126542776
2.2642-2.32540.22951530.172926402793
2.3254-2.39380.2131490.175726542803
2.3938-2.47110.19381430.177926332776
2.4711-2.55940.20151410.179726642805
2.5594-2.66180.22861590.181326402799
2.6618-2.78290.23791430.193326792822
2.7829-2.92960.22151470.193626552802
2.9296-3.11310.2291450.194926922837
3.1131-3.35340.18941340.176526752809
3.3534-3.69070.21571280.15327262854
3.6907-4.22430.19151540.139627112865
4.2243-5.32050.14221330.127427442877
5.3205-41.99190.19561580.159228783036
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)
12.24062.3991-0.07652.79380.1711.01140.2423-0.3321-0.05620.2722-0.18840.0205-0.0680.10850.05130.2581-0.0011-0.01740.4232-0.00120.284110.261319.62134.6097
20.79040.5528-0.22611.0253-0.27440.68740.03350.0223-0.0472-0.1225-0.1122-0.01910.01710.00010.020.22390.0128-0.02690.30990.05070.2513.396816.965813.5208
33.2004-0.7243-1.66270.80791.15653.5161-0.0754-0.1058-0.28620.1177-0.0226-0.05690.28010.59520.12980.37980.0132-0.02460.38550.00780.268321.06128.792115.3557
41.37630.48150.93221.09150.53141.80510.08970.07320.07850.13960.0372-0.035-0.11850.0227-0.14020.2895-0.0005-0.0040.30240.01130.210416.618230.805120.635
50.53660.2572-0.1631.2797-0.5580.76460.0162-0.0113-0.0329-0.0860.07960.17860.0002-0.2153-0.07920.2334-0.0015-0.0350.3410.04780.24983.609613.959116.0534
61.86330.13880.01290.6675-0.0191.046-0.07540.0896-0.1095-0.14060.07670.09690.0747-0.0755-0.00080.2677-0.0211-0.03130.22650.04380.278932.4769-3.399214.9634
71.3111-0.26230.43361.3269-0.51411.955-0.11640.04790.1031-0.00310.11710.0225-0.073-0.12440.02180.2763-0.0102-0.00190.32960.08210.260746.35384.009113.5024
81.7488-0.25580.20740.308-0.14780.97260.0617-0.0763-0.3717-0.0440.05180.12160.2991-0.1128-0.09410.3321-0.0296-0.04390.25880.05030.353129.5778-11.6120.2016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 27 )A0 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 77 )A28 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 95 )A78 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 182 )A96 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 321 )A183 - 321
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 77 )B-1 - 77
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 154 )B78 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 321 )B155 - 321

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