[English] 日本語
Yorodumi
- PDB-8yst: Structure of CylI in complex with beta-ketoacyl-SNAC substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yst
TitleStructure of CylI in complex with beta-ketoacyl-SNAC substrate
ComponentsCylI
KeywordsTRANSFERASE / cyanobacteria / cylindrocyclophane / type III PKS
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid biosynthetic process / membrane
Similarity search - Function
FAE1/Type III polyketide synthase-like protein / FAE1/Type III polyketide synthase-like protein / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Biological speciesCylindrospermum licheniforme UTEX B 2014 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, H.Q. / Xiang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Shenzhen science and technology program20170330155106581 China
Key-Area Research and Development Program of Guangdong Province2020B0303070002 China
CitationJournal: Protein Sci. / Year: 2024
Title: Structural insights into type III polyketide synthase CylI from cylindrocyclophane biosynthesis.
Authors: Wang, H.Q. / Xiang, Z.
History
DepositionMar 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CylI
B: CylI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6813
Polymers86,4552
Non-polymers2261
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.850, 113.441, 134.189
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 CylI / Type III polyketide synthase


Mass: 43227.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermum licheniforme UTEX B 2014 (bacteria)
Gene: cylI / Production host: Escherichia coli (E. coli) / References: UniProt: K7SIG4
#2: Chemical ChemComp-A1D7D / 3-oxidanylidenetetradecanal


Mass: 226.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 27% PEG 4000, 0.09 M Tris-HCl, pH 8.0, 0.18 M magnesium chloride, 3% 1,6-Hexanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→21.51 Å / Num. obs: 59260 / % possible obs: 99.25 % / Redundancy: 4.9 % / Biso Wilson estimate: 14.84 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.12
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 5.66 / Num. unique obs: 5647 / CC1/2: 0.93

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→21.51 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 2948 4.98 %
Rwork0.1933 56308 -
obs0.1951 59256 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 0 16 538 6272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265844
X-RAY DIFFRACTIONf_angle_d0.62497948
X-RAY DIFFRACTIONf_chiral_restr0.0423936
X-RAY DIFFRACTIONf_plane_restr0.00541024
X-RAY DIFFRACTIONf_dihedral_angle_d6.5374805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.26371250.22482561X-RAY DIFFRACTION94.64
1.93-1.960.27641240.21512563X-RAY DIFFRACTION97.07
1.96-20.29011390.21482641X-RAY DIFFRACTION100
2-2.040.25721530.21812674X-RAY DIFFRACTION99.68
2.04-2.080.23871350.20632626X-RAY DIFFRACTION100
2.08-2.130.23621490.21352693X-RAY DIFFRACTION99.86
2.13-2.170.26711320.21122641X-RAY DIFFRACTION100
2.17-2.230.25471280.20452704X-RAY DIFFRACTION100
2.23-2.290.25931490.20542655X-RAY DIFFRACTION100
2.29-2.360.23521370.20822660X-RAY DIFFRACTION99.96
2.36-2.430.24841490.19962699X-RAY DIFFRACTION100
2.43-2.520.24761430.19752665X-RAY DIFFRACTION100
2.52-2.620.24431350.20482671X-RAY DIFFRACTION99.93
2.62-2.740.26111520.20312701X-RAY DIFFRACTION100
2.74-2.880.21941450.20632709X-RAY DIFFRACTION99.96
2.88-3.060.20821250.19532702X-RAY DIFFRACTION99.86
3.06-3.30.21051470.19342691X-RAY DIFFRACTION99.72
3.3-3.630.18711420.17712721X-RAY DIFFRACTION99.44
3.63-4.150.22111430.17332731X-RAY DIFFRACTION99.24
4.15-5.220.18991390.15712740X-RAY DIFFRACTION98.73
5.22-21.510.21791570.17832860X-RAY DIFFRACTION98.31

+
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