[English] 日本語
Yorodumi
- PDB-21ig: Crystal structure of terpeniod cyclase SpSODS from rhizobacterium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 21ig
TitleCrystal structure of terpeniod cyclase SpSODS from rhizobacterium Serratia plymuthica
ComponentsTerpene synthase
KeywordsLYASE / terpeniod cyclase / sodorifen synthase / SpSODS
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 speciesSerratia plymuthica 4Rx13 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLi, X.Q. / Zheng, Y. / Zhang, L.L. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structure and catalytic mechanism of C 16 terpenoid cyclase SpSODS from Serratia plymuthica.
Authors: Li, X. / Zhang, L. / Zheng, Y. / Pan, N. / Zhou, Z. / Huang, Y. / Liang, Q. / Huang, J.W. / Chen, C.C. / Guo, R.T.
History
DepositionDec 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7044
Polymers84,5192
Non-polymers1842
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-21 kcal/mol
Surface area24750 Å2
MethodPISA
2
A: Terpene synthase
hetero molecules

B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7044
Polymers84,5192
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area2640 Å2
ΔGint-15 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.124, 74.874, 142.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Terpene synthase / Sodorifen synthase SpSODS


Mass: 42259.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Saccharomyces cerevisiae is not available during the biocuration, replaced by A0A318P116 temporarily.
Source: (gene. exp.) Serratia plymuthica 4Rx13 (bacteria) / Gene: CT690_00725 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A318P116, 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.21 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26% (w/v) Polyacrylic acid 5100, 0.1 M HEPES, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.22→34.53 Å / Num. obs: 36781 / % possible obs: 99 % / Redundancy: 4.8 % / CC1/2: 0.994 / Net I/σ(I): 7.4
Reflection shellResolution: 2.22→2.26 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1884 / CC1/2: 0.818

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SAINTdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→33.13 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1845 5.09 %RANDOM
Rwork0.1707 ---
obs0.1745 36226 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 12 589 5998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075534
X-RAY DIFFRACTIONf_angle_d0.8487504
X-RAY DIFFRACTIONf_dihedral_angle_d5.79743
X-RAY DIFFRACTIONf_chiral_restr0.049795
X-RAY DIFFRACTIONf_plane_restr0.008981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.30981430.22132484X-RAY DIFFRACTION94
2.28-2.350.26871330.20762546X-RAY DIFFRACTION96
2.35-2.420.26261450.2042574X-RAY DIFFRACTION98
2.42-2.510.27371310.1892616X-RAY DIFFRACTION99
2.51-2.610.26771440.1862635X-RAY DIFFRACTION100
2.61-2.730.28471510.19462653X-RAY DIFFRACTION100
2.73-2.870.26351340.19392658X-RAY DIFFRACTION100
2.87-3.050.28581510.19032649X-RAY DIFFRACTION100
3.05-3.290.24781480.17472679X-RAY DIFFRACTION100
3.29-3.620.25221480.16572668X-RAY DIFFRACTION100
3.62-4.140.25131220.13572719X-RAY DIFFRACTION100
4.14-5.210.18451490.1362731X-RAY DIFFRACTION100
5.21-33.130.20851460.16432769X-RAY DIFFRACTION96

+
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