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- PDB-4pim: Ergothioneine-biosynthetic methyltransferase EgtD, apo form -

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Basic information

Entry
Database: PDB / ID: 4pim
TitleErgothioneine-biosynthetic methyltransferase EgtD, apo form
ComponentsHistidine-specific methyltransferase EgtD
KeywordsTRANSFERASE / methyltransferase / ergothioneine / histidine betaine
Function / homology
Function and homology information


: / 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
ACETATE ION / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsVit, A. / Seebeck, F.P. / Blankenfeldt, W.
Citation
Journal: Chembiochem / Year: 2015
Title: Ergothioneine Biosynthetic Methyltransferase EgtD Reveals the Structural Basis of Aromatic Amino Acid Betaine Biosynthesis.
Authors: Vit, A. / Misson, L. / Blankenfeldt, W. / Seebeck, F.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and preliminary X-ray analysis of the ergothioneine-biosynthetic methyltransferase EgtD
Authors: Vit, A. / Misson, L. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine-specific methyltransferase EgtD
B: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1524
Polymers71,0342
Non-polymers1182
Water15,025834
1
A: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5762
Polymers35,5171
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5762
Polymers35,5171
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.812, 75.500, 138.674
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-specific methyltransferase EgtD / Histidine-alpha-N-methyltransferase


Mass: 35517.172 Da / Num. of mol.: 2 / Mutation: T2A, A29T, P30Q, A75S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 607 / Gene: egtD, MSMEG_6247, MSMEI_6086 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: A0R5M8, L-histidine Nalpha-methyltransferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% w/v PEG8000, 20% w/v glycerol, 0.08 M MES, pH 6.3, 0.16 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.75→41.62 Å / Num. obs: 74530 / % possible obs: 97.4 % / Redundancy: 13.9 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.031 / Net I/σ(I): 15.8 / Num. measured all: 1036396 / Scaling rejects: 194
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.75-1.7814.61.2692.55791039770.34295.8
9.09-41.62130.04845.482346330.01398.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACT3.14data extraction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.75→41.62 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1866 3746 5.03 %
Rwork0.1564 70730 -
obs0.1579 74476 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.56 Å2 / Biso mean: 28.1481 Å2 / Biso min: 4.6 Å2
Refinement stepCycle: final / Resolution: 1.75→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 14 834 5789
Biso mean--40.42 39.16 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095106
X-RAY DIFFRACTIONf_angle_d1.1166957
X-RAY DIFFRACTIONf_chiral_restr0.043800
X-RAY DIFFRACTIONf_plane_restr0.006920
X-RAY DIFFRACTIONf_dihedral_angle_d12.1061854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.77220.26541390.22882530266996
1.7722-1.79550.26951440.22422585272996
1.7955-1.82010.24581230.21342508263196
1.8201-1.84610.24251310.20592589272096
1.8461-1.87360.2051330.18652537267096
1.8736-1.90290.20871220.18282585270796
1.9029-1.93410.24041340.17372590272496
1.9341-1.96750.24221370.17492557269496
1.9675-2.00330.20961290.16762603273296
2.0033-2.04180.1831340.15972571270596
2.0418-2.08350.17471270.15042601272897
2.0835-2.12880.17491590.15132553271297
2.1288-2.17830.17891460.14872605275197
2.1783-2.23280.19781180.1472611272997
2.2328-2.29310.17231410.14232605274697
2.2931-2.36060.19871520.13822598275097
2.3606-2.43680.17041470.14482612275997
2.4368-2.52390.19411300.14782623275398
2.5239-2.62490.19451600.14572592275298
2.6249-2.74440.17471500.15372654280498
2.7444-2.88910.18671380.14912660279898
2.8891-3.070.18871520.15382623277598
3.07-3.3070.19491300.1492685281598
3.307-3.63970.16721330.14562699283298
3.6397-4.16620.18121490.13612731288099
4.1662-5.24790.14221300.13392745287599
5.2479-48.7360.19611580.20652878303699
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)
10.004-0.0075-0.01470.01030.01540.01470.056-0.08540.03120.0597-0.0399-0.03390.01610.091300.2151-0.029-0.03540.21130.00960.19549.835613.965626.7693
20.00260.00160.00050.00170.00270.00270.0258-0.0231-0.0357-0.0038-0.0025-0.0036-0.03870.034700.17970.0003-0.01880.18890.04410.194618.538827.25268.5892
30.01-0.0080.00480.01020.00280.01230.05810.09650.0204-0.03210.0365-0.03870.05680.0585-00.1655-0.0381-0.00570.2546-0.0030.149123.424728.71820.1177
40.04230.0217-0.01010.05-0.00410.06810.0315-0.03050.0040.02420.01430.09470.0046-0.02620.11270.0661-0.0068-0.01450.05540.02550.05554.232216.862217.0831
50.0185-0.00760.00380.00390.00980.0325-0.07630.0059-0.0197-0.10750.0359-0.02780.01660.015100.1927-0.0334-0.02550.18710.03070.211128.8926-5.725910.0793
60.00430.0034-0.00370.00810.00110.0054-0.01040.0010.0374-0.02690.0260.0344-0.02430.0080.00610.15580.0088-0.03810.20220.04380.189243.68731.492824.9543
70.0249-0.03140.02140.0419-0.03220.0266-0.0247-0.02850.02290.07450.0119-0.0283-0.02-0.0128-0.02090.0756-0.0211-0.03150.04190.07990.019945.17895.20113.3818
8-0-0.0004-0.00010.00610.00030.00140.01470.01050.025-0.0296-0.0276-0.00880.0234-0.009400.20080.0065-0.02530.16820.01320.182244.2443-10.766215.7953
90.1110.0115-0.08690.0536-0.01270.1567-0.0875-0.0258-0.0578-0.04810.03350.0650.1235-0.0803-0.17480.0029-0.0012-0.07490.0530.0560.042626.7459-12.263220.6229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 57 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 90 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 145 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 321 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 57 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 90 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 145 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 182 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 183 through 321 )B0

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