[English] 日本語
Yorodumi
- PDB-3wy0: The I375W mutant of CsyB complexed with CoA-SH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wy0
TitleThe I375W mutant of CsyB complexed with CoA-SH
ComponentsPutative uncharacterized protein csyB
KeywordsTRANSFERASE / CsyB / Type III polyketide synthase / Acyltransferase
Function / homology
Function and homology information


type III polyketide synthase complex / tetraketide alpha-pyrone synthase activity / naringenin-chalcone synthase activity / polyketide biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acylalkylpyrone synthase csyB / Acylalkylpyrone synthase csyB
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsMori, T. / Yang, D. / Matsui, T. / Morita, H. / Fujii, I. / Abe, I.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural basis for the formation of acylalkylpyrones from two beta-ketoacyl units by the fungal type III polyketide synthase CsyB.
Authors: Mori, T. / Yang, D. / Matsui, T. / Hashimoto, M. / Morita, H. / Fujii, I. / Abe, I.
History
DepositionAug 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein csyB
B: Putative uncharacterized protein csyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2964
Polymers90,7612
Non-polymers1,5352
Water11,800655
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-5 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.130, 104.560, 73.660
Angle α, β, γ (deg.)90.00, 114.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative uncharacterized protein csyB / Type III polyketide synthase CsyB


Mass: 45380.383 Da / Num. of mol.: 2 / Mutation: I375W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: csyB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: Q53U84, UniProt: Q2U852*PLUS
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM PIPES-NaOH, 6% PEG 4000, 250mM LiCl, 2mM CoA-SH, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 3, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65058 / % possible obs: 99.6 % / Redundancy: 3.81 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.355 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXY

3wxy


Resolution: 2.001→41.244 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 3251 5 %
Rwork0.1709 --
obs0.1726 65034 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→41.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5723 0 96 655 6474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075945
X-RAY DIFFRACTIONf_angle_d1.0688088
X-RAY DIFFRACTIONf_dihedral_angle_d14.3652162
X-RAY DIFFRACTIONf_chiral_restr0.073916
X-RAY DIFFRACTIONf_plane_restr0.0051035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0015-2.03130.25471350.21432573X-RAY DIFFRACTION97
2.0313-2.06310.25121430.20292710X-RAY DIFFRACTION100
2.0631-2.09690.23511390.18952646X-RAY DIFFRACTION100
2.0969-2.13310.2371430.18242714X-RAY DIFFRACTION100
2.1331-2.17180.22541410.19072670X-RAY DIFFRACTION100
2.1718-2.21360.23481390.17472671X-RAY DIFFRACTION100
2.2136-2.25880.19121410.17872666X-RAY DIFFRACTION100
2.2588-2.30790.2221400.17142674X-RAY DIFFRACTION100
2.3079-2.36160.21721420.17722696X-RAY DIFFRACTION100
2.3616-2.42060.20781430.16822701X-RAY DIFFRACTION100
2.4206-2.48610.21971390.17432653X-RAY DIFFRACTION100
2.4861-2.55920.23631420.17072693X-RAY DIFFRACTION100
2.5592-2.64180.20211410.17112674X-RAY DIFFRACTION100
2.6418-2.73620.2111420.16872702X-RAY DIFFRACTION100
2.7362-2.84580.23291410.18082689X-RAY DIFFRACTION100
2.8458-2.97520.2021420.17972685X-RAY DIFFRACTION100
2.9752-3.1320.20831420.17392702X-RAY DIFFRACTION100
3.132-3.32820.21361420.17062697X-RAY DIFFRACTION100
3.3282-3.5850.18941400.16952671X-RAY DIFFRACTION100
3.585-3.94560.1921430.16432715X-RAY DIFFRACTION100
3.9456-4.51590.18231430.14752709X-RAY DIFFRACTION100
4.5159-5.68720.18541440.16162728X-RAY DIFFRACTION100
5.6872-41.25310.1571440.16332744X-RAY DIFFRACTION99

+
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