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

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Basic information

Entry
Database: PDB / ID: 6fnq
TitleErgothioneine-biosynthetic methyltransferase EgtD in complex with N,N,N-trimethylhistidine (hercynine)
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / ergothioneine / methyltransferase / product complex
Function / homology
Function and homology information


N-alpha,N-alpha,N-alpha-trimethyl-L-histidine biosynthesis from histidine / ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / dimethylhistidine N-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
N,N,N-trimethyl-histidine / Histidine N-alpha-methyltransferase / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 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 1.1Mar 20, 2019Group: Data collection / Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)71,53911
Polymers70,5652
Non-polymers9739
Water13,187732
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7826
Polymers35,2831
Non-polymers4995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7575
Polymers35,2831
Non-polymers4754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.040, 79.377, 136.045
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-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
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: 1.75→49.33 Å / Num. obs: 78334 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.039 / Rrim(I) all: 0.145 / Net I/σ(I): 15.3 / Num. measured all: 1046638
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
1.75-1.7813.81.6245891542580.7040.4481.6851.9100
9.09-49.3311.60.03753964910.0090.03258.299.3

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Processing

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

4pim


Resolution: 1.75→49.333 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.64 / Stereochemistry target values: ML / Details: FOURIER SYNTHESIS
RfactorNum. reflection% reflection
Rfree0.1787 3934 5.03 %
Rwork0.152 74319 -
obs0.1534 78253 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.4 Å2 / Biso mean: 26.2681 Å2 / Biso min: 9.69 Å2
Refinement stepCycle: final / Resolution: 1.75→49.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 143 732 5799
Biso mean--45.23 37 -
Num. residues----645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.77140.27451590.244226232782
1.7714-1.79380.27591380.239525872725
1.7938-1.81740.25971320.240126572789
1.8174-1.84230.26571230.220626112734
1.8423-1.86860.2441520.202726332785
1.8686-1.89650.23241320.199926152747
1.8965-1.92610.20091180.184426412759
1.9261-1.95770.20441250.174426162741
1.9577-1.99150.20141300.169426712801
1.9915-2.02770.19121620.162525992761
2.0277-2.06670.18461240.156126262750
2.0667-2.10890.18051350.156326462781
2.1089-2.15470.16121590.142326172776
2.1547-2.20480.15621440.142126322776
2.2048-2.260.17361290.138826652794
2.26-2.32110.14741470.136826302777
2.3211-2.38940.18981450.136326142759
2.3894-2.46650.17171450.14226622807
2.4665-2.55470.18041500.140926552805
2.5547-2.65690.16661520.139926322784
2.6569-2.77780.18391410.136526462787
2.7778-2.92430.16911430.141126502793
2.9243-3.10750.16351350.136426882823
3.1075-3.34740.15441420.132526812823
3.3474-3.68410.15761250.125327072832
3.6841-4.2170.14841550.126927032858
4.217-5.31190.16021360.131527502886
5.3119-49.35240.22021560.216228623018
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)
10.3750.2151-0.3230.9887-0.23941.01250.0488-0.03690.02410.0386-0.0425-0.02910.00060.0455-0.00130.08960.006-0.02310.13230.00630.119111.704318.078621.3454
21.257-0.7537-0.14342.0138-0.41214.82050.14230.0114-0.026-0.01090.0006-0.15680.10810.4241-0.1460.1556-0.0326-0.04750.2308-0.04330.189222.065530.359920.6377
30.37210.04840.04951.2853-0.50570.88260.02330.0055-0.0178-0.02290.01650.0917-0.0278-0.0851-0.05690.10660.0082-0.00220.1548-0.00420.12253.621718.101417.8443
42.04420.0793-0.0490.33860.13421.13610.00530.1044-0.119-0.0621-0.00850.03380.0309-0.0237-0.00860.14260.0167-0.02590.07480.00240.138331.0682-3.425713.8948
51.6907-0.68320.55371.6144-0.08433.6934-0.04070.02520.10670.02820.03140.029-0.031-0.0576-0.00250.1572-0.0113-0.00040.15250.02550.147144.2974.138212.4103
61.7048-0.1295-0.07960.5296-0.15020.6430.01630.0082-0.3524-0.0662-0.0120.11860.1205-0.0335-0.03410.18850.0037-0.02440.1034-0.01550.208226.6407-11.297215.9174
73.0963-0.4384-0.18522.0980.17971.5959-0.0353-0.1213-0.26580.0633-0.0241-0.07880.25480.1380.01410.18020.0432-0.03470.19930.04560.172344.3741-12.094327.5406
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 145 )A78 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 321 )A146 - 321
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 77 )B-1 - 77
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 145 )B78 - 145
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 288 )B146 - 288
7X-RAY DIFFRACTION7chain 'B' and (resid 289 through 321 )B289 - 321

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