[English] 日本語
Yorodumi
- PDB-9bag: Crystal structure of Oryza sativa ketol-acid reductoisomerase in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bag
TitleCrystal structure of Oryza sativa ketol-acid reductoisomerase in complex with Mg2+, and JK-5-114
ComponentsKetol-acid reductoisomerase, chloroplastic
KeywordsISOMERASE / ketol-acid reductoisomerase / Inhibitor / NADPH / 2-acetolactate
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADPH binding / chloroplast / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Ketol-acid reductoisomerase, plant / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Ketol-acid reductoisomerase, chloroplastic
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLin, X. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)114729 Australia
CitationJournal: Chemistry / Year: 2025
Title: A Ketol-Acid Reductoisomerase Inhibitor That Has Antituberculosis and Herbicidal Activity.
Authors: Lin, X. / Kurz, J.L. / Li, Y.H. / Wun, S.J. / Lonhienne, T. / McGeary, R.P. / West, N.P. / Schenk, G. / Wang, J.G. / Guddat, L.W.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ketol-acid reductoisomerase, chloroplastic
B: Ketol-acid reductoisomerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3808
Polymers114,7602
Non-polymers6206
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-58 kcal/mol
Surface area35030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.410, 91.863, 86.998
Angle α, β, γ (deg.)90.000, 101.370, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Ketol-acid reductoisomerase, chloroplastic / Acetohydroxy-acid reductoisomerase / Alpha-keto-beta-hydroxylacyl reductoisomerase / Protein KARI


Mass: 57380.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os05g0573700, LOC_Os05g49800, OJ1735_C10.18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3
References: UniProt: Q65XK0, ketol-acid reductoisomerase (NADP+)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1AKJ / 6-hydroxy-2-phenyl[1,3]thiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione


Mass: 261.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H7N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M NH4SO4 (Salt) 0.1 M BIS-TRIS 6.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 R 1M / Detector: PIXEL / Date: Mar 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.96→46.01 Å / Num. obs: 473997 / % possible obs: 97.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.92 Å2 / Rpim(I) all: 0.035 / Net I/σ(I): 9.9
Reflection shellResolution: 1.96→2 Å / Num. unique obs: 22895 / Rpim(I) all: 0.566 / % possible all: 79.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→45.93 Å / SU ML: 0.2717 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 2000 2.89 %
Rwork0.2128 67154 -
obs0.2135 69154 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.64 Å2
Refinement stepCycle: LAST / Resolution: 1.96→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7347 0 40 297 7684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00467588
X-RAY DIFFRACTIONf_angle_d0.663610277
X-RAY DIFFRACTIONf_chiral_restr0.04191132
X-RAY DIFFRACTIONf_plane_restr0.00541335
X-RAY DIFFRACTIONf_dihedral_angle_d16.82872769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.37571340.34644504X-RAY DIFFRACTION93.91
2.01-2.070.34571440.31144809X-RAY DIFFRACTION99.92
2.07-2.130.28171420.28314793X-RAY DIFFRACTION99.94
2.13-2.20.29271420.27364767X-RAY DIFFRACTION99.9
2.2-2.280.29261430.25184821X-RAY DIFFRACTION100
2.28-2.370.24561440.2354824X-RAY DIFFRACTION99.96
2.37-2.470.27621430.22994809X-RAY DIFFRACTION99.98
2.47-2.610.25821440.22954814X-RAY DIFFRACTION99.98
2.61-2.770.24671420.23664802X-RAY DIFFRACTION99.96
2.77-2.980.28961440.23254819X-RAY DIFFRACTION100
2.98-3.280.22171440.22084821X-RAY DIFFRACTION99.94
3.28-3.760.20921440.20074831X-RAY DIFFRACTION99.9
3.76-4.730.20651440.17464843X-RAY DIFFRACTION99.8
4.73-45.930.22141460.18624897X-RAY DIFFRACTION99.1

+
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