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- PDB-9b9p: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 9b9p
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg2+, and JK-5-114
ComponentsKetol-acid reductoisomerase (NADP(+))
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: 3.18 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: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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
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

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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)76,3938
Polymers75,7732
Non-polymers6206
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-134 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.929, 95.719, 111.356
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: 37886.645 Da / Num. of mol.: 2
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)
References: UniProt: A0A4T9XKD7, ketol-acid reductoisomerase (NADP+)
#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 291 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-5-114 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: 0.953 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 3.176→48.13 Å / Num. obs: 12870 / % possible obs: 97.96 % / Redundancy: 18 % / Biso Wilson estimate: 91.28 Å2 / CC1/2: 0.91 / Net I/σ(I): 8.7
Reflection shellResolution: 3.18→3.29 Å / Num. unique obs: 1066 / CC1/2: 0.801

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→48.13 Å / SU ML: 0.5246 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1561
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2916 1287 10 %
Rwork0.2471 11583 -
obs0.2517 12870 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.88 Å2
Refinement stepCycle: LAST / Resolution: 3.18→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4938 0 40 19 4997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515140
X-RAY DIFFRACTIONf_angle_d0.82746988
X-RAY DIFFRACTIONf_chiral_restr0.0463758
X-RAY DIFFRACTIONf_plane_restr0.0053940
X-RAY DIFFRACTIONf_dihedral_angle_d13.02971839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.30.43021190.41011086X-RAY DIFFRACTION84.38
3.3-3.450.35311420.31471273X-RAY DIFFRACTION99.37
3.45-3.630.35351440.27521284X-RAY DIFFRACTION99.37
3.64-3.860.31821430.28091296X-RAY DIFFRACTION99.58
3.86-4.160.29721430.25451290X-RAY DIFFRACTION99.31
4.16-4.580.29091460.22431303X-RAY DIFFRACTION99.72
4.58-5.240.26541450.22871306X-RAY DIFFRACTION99.93
5.24-6.60.31471480.25971338X-RAY DIFFRACTION99.93
6.6-48.130.24241570.20681407X-RAY DIFFRACTION99.74

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