8KGA

SlNDPS1-AtcPT4 Chimera

• PDB DOI: https://doi.org/10.2210/pdb8KGA/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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.250 
• R-Value Work: 0.203 

Starting Model: experimental

Literature

Biosynthesising various rubber-like polymers by reconstituting prenyltransferases on Hevea rubber particles: molecular and structural bases of the versatile system

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)

Macromolecule Content

• Total Structure Weight: 61.41 kDa 
• Atom Count: 3,920 
• Modelled Residue Count: 470 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2	A, B	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
PEG	C [auth A], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI	F [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.250 
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.11	α = 90
b = 90.107	β = 90
c = 126.479	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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.

---

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

Revision History  

• Version 1.0: 2024-08-21
  Type: Initial release