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- PDB-9bae: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 9bae
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg2+, and JK-5-115
Components(Ketol-acid reductoisomerase (NADP(+))) x 2
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 / isomerase activity / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / 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-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsKurz, J.L. / Lin, X. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)114729 Australia
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D.
History
DepositionApr 3, 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 (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1659
Polymers73,5212
Non-polymers6447
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-137 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.031, 94.353, 96.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase


Mass: 35633.973 Da / Num. of mol.: 1 / Fragment: UN{ 1-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ilvC, CV021_16175, GO782_13585, GO793_08535, GO852_03560, GO941_09745, GZ156_04070, NCTC6133_02793, NCTC7878_02786, NCTC7972_02670, SA950122_01671
Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3
References: UniProt: A0A4T9XKD7, ketol-acid reductoisomerase (NADP+)
#2: Protein Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase


Mass: 37886.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ilvC, CV021_16175, GO782_13585, GO793_08535, GO852_03560, GO941_09745, GZ156_04070, NCTC6133_02793, NCTC7878_02786, NCTC7972_02670, SA950122_01671
Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3
References: UniProt: A0A4T9XKD7, ketol-acid reductoisomerase (NADP+)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1AKY / 6-hydroxy-2-phenyl[1,3]thiazolo[5,4-d]pyrimidine-5,7(4H,6H)-dione


Mass: 261.257 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H7N3O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 0.2 M sodium acetate pH 8.1 35% PEG 3350 0.5 mM JK-5-115 3.5 mM MgCl2 3.5 mM NADPH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.73→48.5 Å / Num. obs: 19410 / % possible obs: 98.5 % / Redundancy: 10 % / Biso Wilson estimate: 59.95 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 10
Reflection shellResolution: 2.73→2.977 Å / Num. unique obs: 2247 / Rpim(I) all: 0.326

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→48.5 Å / SU ML: 0.3854 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2709 1936 9.97 %
Rwork0.2165 17474 -
obs0.2219 19410 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.35 Å2
Refinement stepCycle: LAST / Resolution: 2.73→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 41 41 4852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00474902
X-RAY DIFFRACTIONf_angle_d0.83746638
X-RAY DIFFRACTIONf_chiral_restr0.0616721
X-RAY DIFFRACTIONf_plane_restr0.0061885
X-RAY DIFFRACTIONf_dihedral_angle_d15.09461766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.80.3546950.3046859X-RAY DIFFRACTION69.08
2.8-2.870.34331320.27911256X-RAY DIFFRACTION100
2.87-2.960.31881430.26051243X-RAY DIFFRACTION99.93
2.96-3.050.32881430.26721264X-RAY DIFFRACTION99.93
3.05-3.160.36421330.25421256X-RAY DIFFRACTION99.93
3.16-3.290.32161460.22091258X-RAY DIFFRACTION100
3.29-3.440.26181340.211268X-RAY DIFFRACTION100
3.44-3.620.25681400.20631261X-RAY DIFFRACTION99.93
3.62-3.850.25931420.21351267X-RAY DIFFRACTION99.86
3.85-4.140.27911410.21661280X-RAY DIFFRACTION99.79
4.14-4.560.25041420.19291277X-RAY DIFFRACTION99.93
4.56-5.220.25591410.21221304X-RAY DIFFRACTION99.93
5.22-6.570.28051480.23341308X-RAY DIFFRACTION100
6.57-48.50.21721560.18441373X-RAY DIFFRACTION99.74

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