[English] 日本語
Yorodumi
- PDB-8rxf: Crystal structure of S-SAD phased alpha-keto C-methyl transferase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rxf
TitleCrystal structure of S-SAD phased alpha-keto C-methyl transferase SgvM bound to ketoleucine
ComponentsMethyltransferase
KeywordsTRANSFERASE / S adenosylmethionine-dependent methyltransferases / biocatalysis / C-alkylation
Function / homology
Function and homology information


methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
2-OXO-4-METHYLPENTANOIC ACID / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsGerhardt, S. / Andexer, J.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2024
Title: Structures and protein engineering of the alpha-keto acid C-methyltransferases SgvM and MrsA for rational substrate transfer.
Authors: Sommer-Kamann, C. / Breiltgens, J. / Zou, Z. / Gerhardt, S. / Saleem-Batcha, R. / Kemper, F. / Einsle, O. / Andexer, J.N. / Muller, M.
History
DepositionFeb 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2355
Polymers36,9111
Non-polymers3234
Water3,783210
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,46910
Polymers73,8232
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8430 Å2
ΔGint-120 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.054, 67.054, 183.074
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase


Mass: 36911.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoviridis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R9UTR3

-
Non-polymers , 5 types, 214 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris/HCl pH 8.5, 250 mM Li2SO4, and 23% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.07505 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07505 Å / Relative weight: 1
ReflectionResolution: 2.27→91.54 Å / Num. obs: 20302 / % possible obs: 99.9 % / Redundancy: 171.5 % / CC1/2: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.01 / Rrim(I) all: 0.129 / Net I/σ(I): 50.6
Reflection shellResolution: 2.27→2.39 Å / Rmerge(I) obs: 1.534 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2883 / CC1/2: 0.913 / Rpim(I) all: 0.181 / Rrim(I) all: 1.546

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→62.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.2 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 966 -RANDOM
Rwork0.1869 ---
obs0.189 20228 100 %-
Displacement parametersBiso mean: 62.15 Å2
Baniso -1Baniso -2Baniso -3
1--6.9646 Å20 Å20 Å2
2---6.9646 Å20 Å2
3---13.9292 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.27→62.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 17 210 2793
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072642HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.833593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d897SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes469HARMONIC5
X-RAY DIFFRACTIONt_it2642HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion340SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2273SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion16.87
LS refinement shellResolution: 2.27→2.28 Å
RfactorNum. reflection% reflection
Rfree0.3321 21 -
Rwork0.2951 --
obs0.2969 422 98.09 %
Refinement TLS params.Origin x: 34.0033 Å / Origin y: 10.004 Å / Origin z: -3.2656 Å
111213212223313233
T-0.065 Å20.0459 Å2-0.0128 Å2-0.078 Å2-0.0301 Å2--0.0444 Å2
L0.7725 °20.3574 °20.205 °2-1.2617 °20.2581 °2--1.836 °2
S0.0099 Å °0.0546 Å °0.1464 Å °0.0546 Å °0.0738 Å °0.4268 Å °0.1464 Å °0.4268 Å °-0.0837 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 339
2X-RAY DIFFRACTION1{ A|* }A501 - 505

+
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