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
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wwPDB Validation 3D Report Full Report

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

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	C1K5M2Q56Y11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	D [auth A], E [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B]

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

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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

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release
Version 1.1: 2024-11-13
Changes: Structure summary

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Help and Resources

8KGA

SlNDPS1-AtcPT4 Chimera

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)