8KGB | pdb_00008kgb

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.235 (Depositor), 0.233 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	C1K5M2 Q56Y11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GST (Subject of Investigation/LOI) Query on GST Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	E [auth A], L [auth C], P [auth D]	GERANYL S-THIOLODIPHOSPHATE C₁₀ H₂₀ O₆ P₂ S AKIXWSDUEPPMKM-JXMROGBWSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth C] Focus chain P [auth D]
IPE (Subject of Investigation/LOI) Query on IPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	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		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D]	G [auth A], H [auth B], M [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.235 (Depositor), 0.233 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.191 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(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
Japan Society for the Promotion of Science (JSPS)	Japan	21H02115