[English] 日本語
Yorodumi
- PDB-9bxm: OvoM from Sulfuricurvum sp. isolate STB_99, a SAM-dependent N-met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bxm
TitleOvoM from Sulfuricurvum sp. isolate STB_99, a SAM-dependent N-methyltransferase involved in ovothiol biosynthesis
Components5-thiohistidine N-methyltransferase OvoM
KeywordsTRANSFERASE / ovothiol / S-adenosyl-L-methionine / 5-thiohistidine / 5-selenohistidine
Biological speciesSulfuricurvum sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.27 Å
AuthorsIreland, K.A. / Davis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1937971 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
CitationJournal: Structure / Year: 2025
Title: Structural and functional analysis of SAM-dependent N-methyltransferases involved in ovoselenol and ovothiol biosynthesis.
Authors: Ireland, K.A. / Kayrouz, C.M. / Abbott, M.L. / Seyedsayamdost, M.R. / Davis, K.M.
History
DepositionMay 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-thiohistidine N-methyltransferase OvoM
B: 5-thiohistidine N-methyltransferase OvoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8294
Polymers62,7042
Non-polymers1242
Water4,107228
1
B: 5-thiohistidine N-methyltransferase OvoM
hetero molecules

A: 5-thiohistidine N-methyltransferase OvoM


Theoretical massNumber of molelcules
Total (without water)62,8294
Polymers62,7042
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area3000 Å2
ΔGint-3 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 92.215, 95.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein 5-thiohistidine N-methyltransferase OvoM


Mass: 31352.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfuricurvum sp. (bacteria) / Strain: STB_99 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.5 % / Description: Small plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M citrate pH 5, 24% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→39.62 Å / Num. obs: 28478 / % possible obs: 96.68 % / Redundancy: 1.9 % / Biso Wilson estimate: 37.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03248 / Rpim(I) all: 0.03248 / Rrim(I) all: 0.04593 / Net I/σ(I): 16.63
Reflection shellResolution: 2.27→2.351 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3115 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 2306 / CC1/2: 0.764 / CC star: 0.931 / Rpim(I) all: 0.3115 / Rrim(I) all: 0.4406 / % possible all: 79.83

-
Processing

Software
NameVersionClassification
XDSXDS-Apple_M1data reduction
XDSXDS-Apple_M1data scaling
PHASER1.20.1_4487phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SIR / Resolution: 2.27→39.62 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3296
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 1430 5 %
Rwork0.1869 27145 -
obs0.1893 28475 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.32 Å2
Refinement stepCycle: LAST / Resolution: 2.27→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 8 228 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00433855
X-RAY DIFFRACTIONf_angle_d0.67835223
X-RAY DIFFRACTIONf_chiral_restr0.0469573
X-RAY DIFFRACTIONf_plane_restr0.0066669
X-RAY DIFFRACTIONf_dihedral_angle_d15.82371334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.350.28111160.2292140X-RAY DIFFRACTION77.63
2.35-2.440.29011320.23952493X-RAY DIFFRACTION90.24
2.44-2.550.33051410.22132697X-RAY DIFFRACTION97.09
2.55-2.690.24511430.20512781X-RAY DIFFRACTION99.76
2.69-2.850.24071440.20092774X-RAY DIFFRACTION99.97
2.85-3.070.26481570.21972800X-RAY DIFFRACTION100
3.07-3.380.27841390.20442800X-RAY DIFFRACTION99.97
3.38-3.870.23321480.17932834X-RAY DIFFRACTION99.5
3.87-4.880.18451520.14082836X-RAY DIFFRACTION99.83
4.88-39.620.21141580.18432990X-RAY DIFFRACTION99.87

+
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