9M53 | pdb_00009m53

Crystal structure of 1L-myo-inositol 1-phosphate synthase 1 from Oryza sativa

PDB DOI: https://doi.org/10.2210/pdb9M53/pdb

Classification: ISOMERASE
Organism(s): Oryza sativa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-05 Released: 2026-02-04
Deposition Author(s): Akabane, T., Yota, A., Katoh, E., Hirotsu, N.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.188 (Depositor), 0.197 (DCC)
R-Value Work:
0.148 (Depositor), 0.161 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of 1L-myo-inositol 1-phosphate synthase 1 from Oryza sativa

Akabane, T.

To be published.

Macromolecule Content

Total Structure Weight: 233.19 kDa
Atom Count: 17,695
Modeled Residue Count: 2,025
Deposited Residue Count: 2,064
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol-3-phosphate synthase 1	A, B, C, D	516	Oryza sativa	Mutation(s): 0 Gene Names: RINO1, INO1, INO1-1, Os03g0192700, LOC_Os03g09250 EC: 5.5.1.4
UniProt
Find proteins for O64437 (Oryza sativa subsp. japonica) Explore O64437 Go to UniProtKB: O64437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O64437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain IA [auth D] SDF format, chain M [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain M [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain M [auth B]	AA [auth C], F [auth A], IA [auth D], M [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain IA [auth D] Focus chain M [auth B] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain IA [auth D] Focus chain M [auth B]
KPG Query on KPG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain HA [auth D] SDF format, chain L [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain Z [auth C]	E [auth A], HA [auth D], L [auth B], Z [auth C]	[(3S,4R,5S)-3,4,5,6,6-pentahydroxy-2-oxo-hexyl] dihydrogen phosphate C₆ H₁₃ O₁₀ P GGBBRMAUDBKNLU-WISUUJSJSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth D] Focus chain L [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain HA [auth D] Focus chain L [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth B] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth D], KA [auth D], LA [auth D], MA [auth D], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain PA [auth D] SDF format, chain Y [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Y [auth B]	GA [auth C], K [auth A], PA [auth D], Y [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain K [auth A] Focus chain PA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain GA [auth C] Focus chain K [auth A] Focus chain PA [auth D] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.188 (Depositor), 0.197 (DCC)
R-Value Work: 0.148 (Depositor), 0.161 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.301	α = 90
b = 137.079	β = 90
c = 217.966	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BUCCANEER	model building
Coot	model building
MOLREP	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23K05066
Japan Society for the Promotion of Science (JSPS)	Japan	23KJ1979
Japan Science and Technology	Japan	JPMJSP2159