[English] 日本語
Yorodumi
- PDB-9rs4: Sesterterpene Synthase from Kitasatospora viridis (V57L-Variant, apo) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rs4
TitleSesterterpene Synthase from Kitasatospora viridis (V57L-Variant, apo)
ComponentsTerpene synthase
KeywordsLYASE / Type I Terpene Synthases / Terpene Cyclization Mechanism / Carbocation Cascade / Enzyme Engineering / Active Site Mutagenesis / Chemodiversity
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / Terpene synthase
Function and homology information
Biological speciesKitasatospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLi, H. / Troycke, P. / Yin, Z. / Groll, M. / Dickschat, J.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 (project number 542938137) Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structure-Guided Engineering of a Bacterial Sesterterpene Synthase for Sesterviridene Diversification.
Authors: Li, H. / Troycke, P. / Yin, Z. / Groll, M. / Dickschat, J.S.
History
DepositionJun 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9142
Polymers39,8221
Non-polymers921
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area15390 Å2
Unit cell
Length a, b, c (Å)95.760, 95.760, 112.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

-
Components

#1: Protein Terpene synthase


Mass: 39821.871 Da / Num. of mol.: 1 / Mutation: V57L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora viridis (bacteria) / Gene: FHX73_1760 / Plasmid: pETDuet-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A561SAF2, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M tri-Sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 63132 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.3
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 3 / Num. unique obs: 10063 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.24 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17676 3156 5 %RANDOM
Rwork0.15172 ---
obs0.15297 59963 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.288 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---0.76 Å20 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 6 348 3091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152655
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.6373958
X-RAY DIFFRACTIONr_angle_other_deg1.2151.5726094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77120.667165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98715430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9451527
X-RAY DIFFRACTIONr_chiral_restr0.0570.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8712.4791408
X-RAY DIFFRACTIONr_mcbond_other0.872.4771407
X-RAY DIFFRACTIONr_mcangle_it1.2153.7081767
X-RAY DIFFRACTIONr_mcangle_other1.2153.7091768
X-RAY DIFFRACTIONr_scbond_it0.8332.6891483
X-RAY DIFFRACTIONr_scbond_other0.8332.691484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1313.9682192
X-RAY DIFFRACTIONr_long_range_B_refined2.70630.5153573
X-RAY DIFFRACTIONr_long_range_B_other2.44629.6813486
X-RAY DIFFRACTIONr_rigid_bond_restr0.37535546
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 229 -
Rwork0.229 4354 -
obs--99.98 %

+
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