[English] 日本語
Yorodumi
- PDB-5jgk: Crystal structure of GtmA in complex with SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jgk
TitleCrystal structure of GtmA in complex with SAH
ComponentsUbiE/COQ5 family methyltransferase, putative
KeywordsTRANSFERASE / Aspergillus fumigatus / Methyltransferase / S-ADENOSYL-L-HOMOCYSTEINE / Gliotoxin / Resistance
Function / homologyubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / UbiE/COQ5 family methyltransferase, putative
Function and homology information
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsDolan, S.K. / Bock, T. / Hering, V. / Jones, G.W. / Blankenfeldt, W. / Dolye, S.
CitationJournal: Open Biol / Year: 2017
Title: Structural, mechanistic and functional insight into gliotoxinbis-thiomethylation inAspergillus fumigatus.
Authors: Dolan, S.K. / Bock, T. / Hering, V. / Owens, R.A. / Jones, G.W. / Blankenfeldt, W. / Doyle, S.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UbiE/COQ5 family methyltransferase, putative
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1619
Polymers64,9122
Non-polymers1,2497
Water7,224401
1
A: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0324
Polymers32,4561
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1295
Polymers32,4561
Non-polymers6734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.748, 109.301, 59.856
Angle α, β, γ (deg.)90.000, 112.250, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UbiE/COQ5 family methyltransferase, putative


Mass: 32455.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_02735 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J5Q3C4
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2.4 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.33→45.12 Å / Num. obs: 130776 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Net I/σ(I): 14.4 / Num. measured all: 852355 / Scaling rejects: 196
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.33-1.356.60.896199.1
7.28-45.126.70.04198.6

-
Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→45.117 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.58
RfactorNum. reflection% reflection
Rfree0.1664 6485 4.96 %
Rwork0.1388 --
obs0.1401 130726 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.31 Å2 / Biso mean: 22.3843 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 1.33→45.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 115 401 4888
Biso mean--22.17 29.92 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074651
X-RAY DIFFRACTIONf_angle_d1.0246381
X-RAY DIFFRACTIONf_chiral_restr0.077726
X-RAY DIFFRACTIONf_plane_restr0.007815
X-RAY DIFFRACTIONf_dihedral_angle_d18.7081683
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 (%)
1.33-1.34510.24572190.20014085430499
1.3451-1.36090.21982490.19524163441299
1.3609-1.37750.24462230.18814083430699
1.3775-1.3950.22212320.17714204443699
1.395-1.41330.22772210.16444096431799
1.4133-1.43270.21732260.16024159438599
1.4327-1.45320.20961920.15084121431398
1.4532-1.47490.17812060.1444077428397
1.4749-1.49790.17422180.13254188440699
1.4979-1.52250.1482230.11784170439399
1.5225-1.54870.14471940.11024130432499
1.5487-1.57690.1632340.11554238447299
1.5769-1.60720.16452120.1144105431799
1.6072-1.640.14952150.11244137435299
1.64-1.67570.15372200.114149436999
1.6757-1.71470.14611980.11354137433598
1.7147-1.75750.15192200.11934103432398
1.7575-1.80510.18712300.11914180441099
1.8051-1.85820.15552110.11894157436899
1.8582-1.91820.15812250.12164165439099
1.9182-1.98670.17312210.1244147436899
1.9867-2.06630.17312090.12914162437199
2.0663-2.16030.16312120.13024104431698
2.1603-2.27420.15182000.12734102430297
2.2742-2.41670.16381810.13164200438199
2.4167-2.60330.1592180.14024199441799
2.6033-2.86520.17262190.154140435999
2.8652-3.27970.1741960.15994020421695
3.2797-4.13160.16642280.14494169439799
4.1316-45.14290.15042330.15044151438497

+
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