[English] 日本語
Yorodumi
- PDB-6fnq: Ergothioneine-biosynthetic methyltransferase EgtD in complex with... -

+
Open data


ID or keywords:

Loading...

-
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


: / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://pdbjlvh1.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