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- PDB-4pio: Ergothioneine-biosynthetic methyltransferase EgtD in complex with... -

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Basic information

Entry
Database: PDB / ID: 4pio
TitleErgothioneine-biosynthetic methyltransferase EgtD in complex with N,N-dimethylhistidine and SAH
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
N,N-dimethyl-L-histidine / S-ADENOSYL-L-HOMOCYSTEINE / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.506 Å
AuthorsVit, A. / Seebeck, F.P. / Blankenfeldt, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Foundation147005 Switzerland
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_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_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 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3Sep 27, 2023Group: 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 / refine_hist / struct_conn / struct_conn_type
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_asym_id / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)71,94613
Polymers70,6292
Non-polymers1,31711
Water17,745985
1
A: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0158
Polymers35,3151
Non-polymers7007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9315
Polymers35,3151
Non-polymers6164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.709, 67.511, 79.679
Angle α, β, γ (deg.)90.000, 110.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histidine-specific methyltransferase EgtD / Histidine-alpha-N-methyltransferase


Mass: 35314.695 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)
References: UniProt: A0R5M8, L-histidine Nalpha-methyltransferase

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Non-polymers , 5 types, 996 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-AVI / N,N-dimethyl-L-histidine


Mass: 183.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N3O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.506→49.995 Å / Num. all: 87536 / Num. obs: 87536 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 10.76 Å2 / Rpim(I) all: 0.059 / Rrim(I) all: 0.106 / Rsym value: 0.088 / Net I/av σ(I): 5.942 / Net I/σ(I): 8.9 / Num. measured all: 275925
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.51-1.593.10.5511.438056123540.3690.551295.9
1.59-1.683.20.41.938120120280.2650.42.798.5
1.68-1.83.20.2812.735833113000.1860.2813.898.9
1.8-1.943.20.185433516105720.1220.1855.799.1
1.94-2.133.20.1166.13105897730.0770.1168.899.4
2.13-2.383.20.0833.32816688820.0550.08311.899.7
2.38-2.753.20.06510.82497078950.0430.06514.199.8
2.75-3.373.20.0512.32101466510.0340.0518.6100
3.37-4.763.10.03715.21629851890.0250.03724.4100
4.76-49.9953.10.03414.7889428920.0230.03423.299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
SCALA3.3.21data scaling
MOLREPphasing
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PIM

4pim


Resolution: 1.506→49.995 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 4356 4.98 %
Rwork0.1481 83153 -
obs0.1497 87509 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.3 Å2 / Biso mean: 15.5812 Å2 / Biso min: 2.53 Å2
Refinement stepCycle: final / Resolution: 1.506→49.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 148 985 5956
Biso mean--9.2 27.1 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085116
X-RAY DIFFRACTIONf_angle_d1.2786981
X-RAY DIFFRACTIONf_chiral_restr0.047795
X-RAY DIFFRACTIONf_plane_restr0.007918
X-RAY DIFFRACTIONf_dihedral_angle_d12.6771892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5064-1.52350.27491120.24072439255187
1.5235-1.54140.27481410.22522752289398
1.5414-1.56020.22961510.21672751290298
1.5602-1.580.26661360.21262741287798
1.58-1.60080.24791460.21362760290698
1.6008-1.62270.26391260.20712765289198
1.6227-1.64590.25031370.19152735287298
1.6459-1.67040.20321530.19522752290598
1.6704-1.69650.25151570.18662742289998
1.6965-1.72440.20791580.18072771292999
1.7244-1.75410.22421470.17282710285799
1.7541-1.7860.21591470.16592759290699
1.786-1.82040.22841520.16362791294399
1.8204-1.85750.17581400.15432778291899
1.8575-1.89790.18361440.15862774291899
1.8979-1.94210.17021310.15212790292199
1.9421-1.99060.20941290.15262796292599
1.9906-2.04440.18291370.14722815295299
2.0444-2.10460.16411590.1362748290799
2.1046-2.17250.16331450.13182801294699
2.1725-2.25020.1581800.129227452925100
2.2502-2.34030.16551430.12482814295799
2.3403-2.44680.1821580.127527942952100
2.4468-2.57580.17741360.132228132949100
2.5758-2.73710.16441310.135528132944100
2.7371-2.94850.18031350.140428382973100
2.9485-3.24510.15071500.129528072957100
3.2451-3.71460.14851550.122728282983100
3.7146-4.67940.14041650.115328563021100
4.6794-50.02250.16191550.1592875303099

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