[English] 日本語
Yorodumi
- PDB-9gdj: C-Methyltransferase SgMT from Streptomyces griseoviridis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gdj
TitleC-Methyltransferase SgMT from Streptomyces griseoviridis
ComponentsMethyltransferase
KeywordsTRANSFERASE / methyl transfer / pyrroloindole synthesis / Rossmann fold / S-adenosyl methionine
Function / homologyISOPROPYL ALCOHOL / COBALT HEXAMMINE(III) / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWeiergraeber, O.H. / Haase, M. / Pietruszka, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem Sci / Year: 2025
Title: Characterization of a C-methyltransferase from Streptomyces griseoviridis - crystal structure, mechanism, and substrate scope.
Authors: Haase, M. / Weiergraber, O.H. / David, B. / Pfirmann, E.L. / Paschold, B. / Gohlke, H. / Pietruszka, J.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,33948
Polymers96,2393
Non-polymers5,10045
Water14,268792
1
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,28929
Polymers64,1602
Non-polymers3,13027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint1 kcal/mol
Surface area22900 Å2
MethodPISA
2
C: Methyltransferase
hetero molecules

C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,10038
Polymers64,1602
Non-polymers3,94036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8680 Å2
ΔGint12 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.920, 123.920, 126.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-569-

HOH

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Methyltransferase


Mass: 32079.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GenBank entry WP_189425200.1 / Source: (gene. exp.) Streptomyces griseoviridis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 7 types, 837 molecules

#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: sodium citrate, PEG 4000, 2-propanol, glycerol, hexammine cobalt(III) chloride, S-adenosyl homocysteine, cyclo(Trp-Trp)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.47→37.43 Å / Num. obs: 166186 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 23.75 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.113 / Net I/σ(I): 11.65
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 13.17 % / Mean I/σ(I) obs: 0.78 / Num. unique obs: 12132 / CC1/2: 0.347 / Rrim(I) all: 3.287 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→37.43 Å / SU ML: 0.1766 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1749 3324 2 %
Rwork0.1471 162852 -
obs0.1477 166176 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.47→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 238 792 7243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057331
X-RAY DIFFRACTIONf_angle_d0.7410005
X-RAY DIFFRACTIONf_chiral_restr0.07731059
X-RAY DIFFRACTIONf_plane_restr0.00771343
X-RAY DIFFRACTIONf_dihedral_angle_d13.08532746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.490.36051360.3086674X-RAY DIFFRACTION99.65
1.49-1.510.32951380.28086733X-RAY DIFFRACTION100
1.51-1.540.28591360.2646671X-RAY DIFFRACTION99.99
1.54-1.560.30491370.25196707X-RAY DIFFRACTION99.99
1.56-1.590.2491370.23276754X-RAY DIFFRACTION100
1.59-1.620.28841360.21936663X-RAY DIFFRACTION100
1.62-1.650.22551380.20326758X-RAY DIFFRACTION99.94
1.65-1.680.25261380.17746735X-RAY DIFFRACTION100
1.68-1.720.22951370.16716730X-RAY DIFFRACTION100
1.72-1.760.21181380.15416735X-RAY DIFFRACTION99.97
1.76-1.80.1961360.1486708X-RAY DIFFRACTION100
1.8-1.850.19341380.14076759X-RAY DIFFRACTION100
1.85-1.910.1941390.13786775X-RAY DIFFRACTION100
1.91-1.970.17221380.13486762X-RAY DIFFRACTION100
1.97-2.040.1511380.12556771X-RAY DIFFRACTION100
2.04-2.120.14751370.12516742X-RAY DIFFRACTION100
2.12-2.220.16621390.12756792X-RAY DIFFRACTION100
2.22-2.330.16751390.13256793X-RAY DIFFRACTION100
2.33-2.480.16711390.13746830X-RAY DIFFRACTION100
2.48-2.670.17741390.14486795X-RAY DIFFRACTION100
2.67-2.940.14541400.14076866X-RAY DIFFRACTION100
2.94-3.360.15341400.14016883X-RAY DIFFRACTION100
3.36-4.240.14541430.13246971X-RAY DIFFRACTION99.99
4.24-37.430.18941480.15347245X-RAY DIFFRACTION99.92

+
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