8KGB

SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP

• PDB DOI: https://doi.org/10.2210/pdb8KGB/pdb

• Classification: TRANSFERASE
• Organism(s): Solanum lycopersicum, Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-18 Released: 2024-08-21 
• Deposition Author(s): Suenaga-Hiromori, M., Ishii, T., Imaizumi, R., Takeshita, K., Yanai, T., Matsuura, H., Sakai, N., Yamaguchi, H., Yanbe, F., Waki, T., Tozawa, Y., Miyagi-Inoue, Y., Yamamoto, M., Kataoka, K., Nakayama, T., Yamashita, S., Takahashi, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.235 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

A versatile system for enzymatic synthesis of natural and unnatural polyisoprenoids on rubber particles

Suenaga-Hiromori, M., Ishii, T., Imaizumi, R., Takeshita, K., Yanai, T., Matsuura, H., Sakai, N., Mikami, T., Takahashi, T., Minakawa, C., Yamaguchi, H., Yanbe, F., Waki, T., Tozawa, Y., Miyagi-Inoue, Y., Fushihara, K., Yamamoto, M., Kataoka, K., Nakayama, T., Yamashita, S., Takahashi, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 123.93 kDa 
• Atom Count: 8,200 
• Modelled Residue Count: 973 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2	A, B, C, D	265	Solanum lycopersicum, Arabidopsis thaliana	Mutation(s): 0  Gene Names: CPT1, NDPS1, At5g58770 EC: 2.5.1.28 (PDB Primary Data), 2.5.1 (UniProt)
UniProt
Find proteins for C1K5M2 (Solanum lycopersicum) Explore C1K5M2  Go to UniProtKB:  C1K5M2
Find proteins for Q56Y11 (Arabidopsis thaliana) Explore Q56Y11  Go to UniProtKB:  Q56Y11
UniProt Groups	C1K5M2Q56Y11

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GST (Subject of Investigation/LOI)	E [auth A], L [auth C], P [auth D]	GERANYL S-THIOLODIPHOSPHATE C10 H20 O6 P2 S AKIXWSDUEPPMKM-JXMROGBWSA-N
IPE (Subject of Investigation/LOI)	F [auth A], I [auth B], J [auth B], K [auth C], O [auth D]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	G [auth A], H [auth B], M [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.235 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.54	α = 90
b = 126.71	β = 90.25
c = 72.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
DIALS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-21 
Deposition Author(s): Suenaga-Hiromori, M., Ishii, T., Imaizumi, R., Takeshita, K., Yanai, T., Matsuura, H., Sakai, N., Yamaguchi, H., Yanbe, F., Waki, T., Tozawa, Y., Miyagi-Inoue, Y., Yamamoto, M., Kataoka, K., Nakayama, T., Yamashita, S., Takahashi, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H05470
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101070
Japan Society for the Promotion of Science (JSPS)	Japan	22K19143
Japan Society for the Promotion of Science (JSPS)	Japan	22KJ1466
Japan Society for the Promotion of Science (JSPS)	Japan	20H02909
Japan Society for the Promotion of Science (JSPS)	Japan	21H02115

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary