[English] 日本語
Yorodumi
- PDB-9j0c: Site-Specific Introduction of Sulfoxides and Sulfones into Polyke... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j0c
TitleSite-Specific Introduction of Sulfoxides and Sulfones into Polyketide Scaffold through a Relayed Chemo-Biosynthetic Strategy
ComponentsAcyl-CoA carboxylase subunit beta
KeywordsBIOSYNTHETIC PROTEIN / polyketide / biosynthesis / sulfoxides / sulfones / extender units
Function / homology
Function and homology information


propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process
Similarity search - Function
Acetyl-CoA carboxylase carboxyl transferase, beta subunit / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Acyl-CoA carboxylase subunit beta
Similarity search - Component
Biological speciesStreptomyces armeniacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, J. / Qu, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200033 China
CitationJournal: ACS Catal. / Year: 2025
Title: Site-Specific Introduction of Sulfoxides and Sulfones into Polyketide Scaffolds through a Relayed Chemo-Biosynthetic Strategy
Authors: Zhang, J. / Zeng, X. / Chen, H. / Yun, Q. / Tian, W. / Du, Y. / Lin, Z. / Lei, C. / Deng, Z. / Qu, X.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl-CoA carboxylase subunit beta


Theoretical massNumber of molelcules
Total (without water)57,5071
Polymers57,5071
Non-polymers00
Water10,701594
1
A: Acyl-CoA carboxylase subunit beta
x 6


Theoretical massNumber of molelcules
Total (without water)345,0436
Polymers345,0436
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area44640 Å2
ΔGint-199 kcal/mol
Surface area106180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.040, 124.040, 134.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-1089-

HOH

-
Components

#1: Protein Acyl-CoA carboxylase subunit beta


Mass: 57507.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces armeniacus (bacteria) / Gene: DVA86_18240 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A345XRN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 and 30% v/v MPD, 0.1 M imidazole, pH 7.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.96183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96183 Å / Relative weight: 1
ReflectionResolution: 1.6→34.76 Å / Num. obs: 80119 / % possible obs: 99.4 % / Redundancy: 17.3 % / CC1/2: 1 / Net I/σ(I): 37.6
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 3737 / CC1/2: 0.891

-
Processing

Software
NameVersionClassification
PHENIX1.21.1.5286refinement
xia2data reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.76 Å / SU ML: 0.1389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.6865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1843 1999 2.5 %
Rwork0.1721 78098 -
obs0.1724 80097 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 0 594 4425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643895
X-RAY DIFFRACTIONf_angle_d0.80465281
X-RAY DIFFRACTIONf_chiral_restr0.0547607
X-RAY DIFFRACTIONf_plane_restr0.009697
X-RAY DIFFRACTIONf_dihedral_angle_d15.49961431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.25941340.21275263X-RAY DIFFRACTION95.05
1.64-1.680.23191370.18975339X-RAY DIFFRACTION96.71
1.68-1.730.1641410.18115487X-RAY DIFFRACTION99.4
1.73-1.790.21361420.1765532X-RAY DIFFRACTION99.98
1.79-1.850.19561420.17185562X-RAY DIFFRACTION100
1.85-1.930.18311420.17495539X-RAY DIFFRACTION100
1.93-2.020.20721430.17315570X-RAY DIFFRACTION100
2.02-2.120.18471420.16825560X-RAY DIFFRACTION100
2.12-2.250.19781430.16775597X-RAY DIFFRACTION100
2.25-2.430.19331440.17065601X-RAY DIFFRACTION100
2.43-2.670.15761440.17365608X-RAY DIFFRACTION100
2.67-3.060.18061450.17045690X-RAY DIFFRACTION100
3.06-3.850.16341470.16075735X-RAY DIFFRACTION99.98
3.85-32.10.18651530.17626015X-RAY DIFFRACTION99.97

+
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