[English] 日本語
Yorodumi
- PDB-8yl9: Crystal structures of terpene synthases complexed with a substrat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yl9
TitleCrystal structures of terpene synthases complexed with a substrate mimic
ComponentsSesterbrasiliatriene synthase PbSS
KeywordsBIOSYNTHETIC PROTEIN / sesterterpene synthase / terpene cyclase / sesterbrasiliatriene synthase
Function / homology
Function and homology information


geranylfarnesyl diphosphate synthase / alcohol biosynthetic process / Lyases; Carbon-oxygen lyases; Acting on phosphates / ketone biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / prenyltransferase activity / terpenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function
Terpene synthase family 2, C-terminal metal binding / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE / Sesterbrasiliatriene synthase PbSS
Similarity search - Component
Biological speciesPenicillium brasilianum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsXu, M. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structural Insights Into the Terpene Cyclization Domains of Two Fungal Sesterterpene Synthases and Enzymatic Engineering for Sesterterpene Diversification.
Authors: Xu, M. / Xu, H. / Lei, Z. / Xing, B. / Dickschat, J.S. / Yang, D. / Ma, M.
History
DepositionMar 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sesterbrasiliatriene synthase PbSS
B: Sesterbrasiliatriene synthase PbSS
I: Sesterbrasiliatriene synthase PbSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,30018
Polymers120,9703
Non-polymers1,33015
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sesterbrasiliatriene synthase PbSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7676
Polymers40,3231
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-35 kcal/mol
Surface area15610 Å2
MethodPISA
3
B: Sesterbrasiliatriene synthase PbSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7676
Polymers40,3231
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-34 kcal/mol
Surface area15010 Å2
MethodPISA
4
I: Sesterbrasiliatriene synthase PbSS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7676
Polymers40,3231
Non-polymers4435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-31 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.990, 146.990, 146.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

-
Components

#1: Protein Sesterbrasiliatriene synthase PbSS / Bifunctional sesterterpene synthase PbSS / SS


Mass: 40323.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium brasilianum (fungus) / Gene: PbSS / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2Z6AQX7, Lyases; Carbon-oxygen lyases; Acting on phosphates, geranylgeranyl diphosphate synthase, geranylfarnesyl diphosphate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 200 mM Magnesium formate and 26% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97902 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.75→44.32 Å / Num. obs: 27686 / % possible obs: 99.6 % / Redundancy: 36.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 27.8
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 0.515 / Num. unique obs: 3987

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→44.32 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 1994 7.21 %
Rwork0.1871 --
obs0.193 27648 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 78 165 8555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138578
X-RAY DIFFRACTIONf_angle_d1.22211584
X-RAY DIFFRACTIONf_dihedral_angle_d19.5843132
X-RAY DIFFRACTIONf_chiral_restr0.0731206
X-RAY DIFFRACTIONf_plane_restr0.0081489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.34861410.21551804X-RAY DIFFRACTION99
2.82-2.890.28361430.22231804X-RAY DIFFRACTION99
2.9-2.980.34641350.23241806X-RAY DIFFRACTION99
2.98-3.080.33361360.22291823X-RAY DIFFRACTION100
3.08-3.190.34291440.21671817X-RAY DIFFRACTION99
3.19-3.310.32681420.21961802X-RAY DIFFRACTION99
3.32-3.460.30041460.20181829X-RAY DIFFRACTION99
3.47-3.650.2891420.19561823X-RAY DIFFRACTION100
3.65-3.870.23741390.17621812X-RAY DIFFRACTION99
3.88-4.170.24921420.15841829X-RAY DIFFRACTION99
4.18-4.590.21631460.15841841X-RAY DIFFRACTION100
4.6-5.260.22171400.1671845X-RAY DIFFRACTION100
5.26-6.620.25421440.18961878X-RAY DIFFRACTION100
6.63-44.320.20291540.15421941X-RAY DIFFRACTION100

+
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