[English] 日本語
Yorodumi
- PDB-4pio: Ergothioneine-biosynthetic methyltransferase EgtD in complex with... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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
Revision 2.0Nov 13, 2024Group: Atomic model / Data collection / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 996 molecules

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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more