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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fnt
TitleErgothioneine-biosynthetic methyltransferase EgtD in complex with pyrrolidinohistidine
ComponentsHistidine N-alpha-methyltransferase
KeywordsTRANSFERASE / ergothioneine / methyltransferase / inhibitor 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
Pyrrolidinohistidine / Histidine N-alpha-methyltransferase / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)70,9884
Polymers70,5652
Non-polymers4232
Water5,567309
1
A: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4942
Polymers35,2831
Non-polymers2111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine N-alpha-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4942
Polymers35,2831
Non-polymers2111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.768, 77.535, 139.045
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-AVO / Pyrrolidinohistidine


Mass: 211.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
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: 1.9→49.25 Å / Num. obs: 61947 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 29.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.089 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.9413.81.38239550.8250.3821.434100
9.11-49.2510.50.036560.9990.0090.03199.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PIM
Resolution: 1.9→41.982 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.01 / Details: FOURIER SYNTHESIS
RfactorNum. reflection% reflection
Rfree0.2071 3107 5.02 %
Rwork0.1701 --
obs0.172 61858 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 244.52 Å2 / Biso mean: 44.6038 Å2 / Biso min: 22.22 Å2
Refinement stepCycle: final / Resolution: 1.9→41.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4919 0 60 309 5288
Biso mean--42.51 45.12 -
Num. residues----645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045080
X-RAY DIFFRACTIONf_angle_d0.8766917
X-RAY DIFFRACTIONf_chiral_restr0.033797
X-RAY DIFFRACTIONf_plane_restr0.004909
X-RAY DIFFRACTIONf_dihedral_angle_d13.1341830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.92970.37031180.28926542772
1.9297-1.96130.3121340.260926412775
1.9613-1.99520.29371420.24626402782
1.9952-2.03140.27671390.221926092748
2.0314-2.07050.26441370.209226302767
2.0705-2.11280.20921250.1926762801
2.1128-2.15870.2291690.188326302799
2.1587-2.20890.21081340.186226262760
2.2089-2.26420.23771220.177126542776
2.2642-2.32540.22951530.172926402793
2.3254-2.39380.2131490.175726542803
2.3938-2.47110.19381430.177926332776
2.4711-2.55940.20151410.179726642805
2.5594-2.66180.22861590.181326402799
2.6618-2.78290.23791430.193326792822
2.7829-2.92960.22151470.193626552802
2.9296-3.11310.2291450.194926922837
3.1131-3.35340.18941340.176526752809
3.3534-3.69070.21571280.15327262854
3.6907-4.22430.19151540.139627112865
4.2243-5.32050.14221330.127427442877
5.3205-41.99190.19561580.159228783036
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.24062.3991-0.07652.79380.1711.01140.2423-0.3321-0.05620.2722-0.18840.0205-0.0680.10850.05130.2581-0.0011-0.01740.4232-0.00120.284110.261319.62134.6097
20.79040.5528-0.22611.0253-0.27440.68740.03350.0223-0.0472-0.1225-0.1122-0.01910.01710.00010.020.22390.0128-0.02690.30990.05070.2513.396816.965813.5208
33.2004-0.7243-1.66270.80791.15653.5161-0.0754-0.1058-0.28620.1177-0.0226-0.05690.28010.59520.12980.37980.0132-0.02460.38550.00780.268321.06128.792115.3557
41.37630.48150.93221.09150.53141.80510.08970.07320.07850.13960.0372-0.035-0.11850.0227-0.14020.2895-0.0005-0.0040.30240.01130.210416.618230.805120.635
50.53660.2572-0.1631.2797-0.5580.76460.0162-0.0113-0.0329-0.0860.07960.17860.0002-0.2153-0.07920.2334-0.0015-0.0350.3410.04780.24983.609613.959116.0534
61.86330.13880.01290.6675-0.0191.046-0.07540.0896-0.1095-0.14060.07670.09690.0747-0.0755-0.00080.2677-0.0211-0.03130.22650.04380.278932.4769-3.399214.9634
71.3111-0.26230.43361.3269-0.51411.955-0.11640.04790.1031-0.00310.11710.0225-0.073-0.12440.02180.2763-0.0102-0.00190.32960.08210.260746.35384.009113.5024
81.7488-0.25580.20740.308-0.14780.97260.0617-0.0763-0.3717-0.0440.05180.12160.2991-0.1128-0.09410.3321-0.0296-0.04390.25880.05030.353129.5778-11.6120.2016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 27 )A0 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 77 )A28 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 95 )A78 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 182 )A96 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 321 )A183 - 321
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 77 )B-1 - 77
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 154 )B78 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 321 )B155 - 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://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