[English] 日本語
Yorodumi
- PDB-9m53: Crystal structure of 1L-myo-inositol 1-phosphate synthase 1 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9m53
TitleCrystal structure of 1L-myo-inositol 1-phosphate synthase 1 from Oryza sativa
ComponentsInositol-3-phosphate synthase 1
KeywordsISOMERASE / 1L-myo-inositol 1-phosphate synthase 1
Function / homology
Function and homology information


inositol-3-phosphate synthase / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / nucleus / cytoplasm / cytosol
Similarity search - Function
Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Chem-KPG / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Inositol-3-phosphate synthase 1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsAkabane, T. / Yota, A. / Katoh, E. / Hirotsu, N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05066 Japan
Japan Society for the Promotion of Science (JSPS)23KJ1979 Japan
Japan Science and TechnologyJPMJSP2159 Japan
CitationJournal: Nat Food / Year: 2026
Title: Chemical inhibition of INO1 reduces phytic acid in rice and wheat grains for enhanced micronutrient bioavailability.
Authors: Akabane, T. / Kamino, S. / Okamura, T. / Sugaya, A. / Nakamura, M. / Ikeda, K. / Yonezawa, T. / Fukushima, A. / Kojima, S. / Aoki, Y. / Chujo, S. / Yamauchi, Y. / Shibusawa, R. / Ishimaru, K. ...Authors: Akabane, T. / Kamino, S. / Okamura, T. / Sugaya, A. / Nakamura, M. / Ikeda, K. / Yonezawa, T. / Fukushima, A. / Kojima, S. / Aoki, Y. / Chujo, S. / Yamauchi, Y. / Shibusawa, R. / Ishimaru, K. / Nagasaka, S. / Katoh, E. / Hirotsu, N.
History
DepositionMar 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inositol-3-phosphate synthase 1
B: Inositol-3-phosphate synthase 1
C: Inositol-3-phosphate synthase 1
D: Inositol-3-phosphate synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,18742
Polymers227,6514
Non-polymers5,53638
Water29,8511657
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37970 Å2
ΔGint-140 kcal/mol
Surface area62540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.301, 137.079, 217.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Inositol-3-phosphate synthase 1 / MIP synthase 1 / Myo-inositol 1-phosphate synthase / IPS / MI-1-P synthase / OsINO1-1


Mass: 56912.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: RINO1, INO1, INO1-1, Os03g0192700, LOC_Os03g09250 / Production host: Escherichia coli (E. coli) / References: UniProt: O64437, inositol-3-phosphate synthase

-
Non-polymers , 5 types, 1695 molecules

#2: Chemical
ChemComp-KPG / [(3S,4R,5S)-3,4,5,6,6-pentahydroxy-2-oxo-hexyl] dihydrogen phosphate


Mass: 276.135 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O10P
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1657 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Magnesium chloride hexahydrate, 0.1M Tris-HCl at pH8.0 and 25% (w/v) Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.012 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.012 Å / Relative weight: 1
ReflectionResolution: 1.79→49.08 Å / Num. obs: 198484 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.187 / Net I/σ(I): 10.3
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9673 / CC1/2: 0.652 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
BUCCANEERmodel building
Cootmodel building
MOLREPphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→47.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.475 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18833 10011 5 %RANDOM
Rwork0.14794 ---
obs0.14996 188357 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.12 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.79→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15686 0 352 1657 17695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01216322
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615555
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.81622129
X-RAY DIFFRACTIONr_angle_other_deg0.7321.74735940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02152018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.929591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.971102795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.22548
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023467
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4671.1728093
X-RAY DIFFRACTIONr_mcbond_other1.4671.1718093
X-RAY DIFFRACTIONr_mcangle_it2.0222.09710104
X-RAY DIFFRACTIONr_mcangle_other2.0222.09710105
X-RAY DIFFRACTIONr_scbond_it2.9981.4758229
X-RAY DIFFRACTIONr_scbond_other2.9981.4758230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3962.54712026
X-RAY DIFFRACTIONr_long_range_B_refined5.46813.2718834
X-RAY DIFFRACTIONr_long_range_B_other5.46913.2718835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 721 -
Rwork0.23 13761 -
obs--99.99 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more