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- PDB-9bag: Crystal structure of Oryza sativa ketol-acid reductoisomerase in ... -

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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: Guddat, L.W. / Lin, X. / Kurz, J.L. / Li, Y.H. / Wun, S.J. / Lonhienne, T. / McGeary, R.P. / West, N.P. / Schenk, G. / Wang, J.G.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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)

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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

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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

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