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- PDB-7ke2: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 7ke2
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg2+ and NSC116565
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE / Oxidoreductase / REDUCTOISOMERASE / INHIBITOR / METAL BINDING PROTEIN
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
Chem-WBY / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsKurz, J.L. / Patel, K.P. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)114729 Australia
CitationJournal: Chemistry / Year: 2021
Title: Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol-Acid Reductoisomerase.
Authors: Lin, X. / Kurz, J.L. / Patel, K.M. / Wun, S.J. / Hussein, W.M. / Lonhienne, T. / West, N.P. / McGeary, R.P. / Schenk, G. / Guddat, L.W.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ketol-acid reductoisomerase (NADP(+))
A: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2698
Polymers75,7732
Non-polymers4966
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-125 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.446, 94.063, 97.203
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, BMF23_13825, BO217_1422, ERS072840_02559 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A145BYP4, 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-WBY / 6-hydroxy-2-methyl[1,3]thiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione


Mass: 199.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: 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

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 289.5 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 0.2 M sodium acetate pH 8.1, 32.5% PEG3350

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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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.59→43.18 Å / Num. obs: 22965 / % possible obs: 99.5 % / Redundancy: 6.58 % / Biso Wilson estimate: 48.62 Å2 / Rpim(I) all: 0.042 / Net I/σ(I): 11.6
Reflection shellResolution: 2.59→2.68 Å / Num. unique obs: 2131 / Rpim(I) all: 0.431 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w3k

5w3k


Resolution: 2.59→43.18 Å / SU ML: 0.3858 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.5691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2786 2005 8.77 %
Rwork0.2356 20845 -
obs0.2394 22850 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.88 Å2
Refinement stepCycle: LAST / Resolution: 2.59→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4871 0 30 41 4942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244994
X-RAY DIFFRACTIONf_angle_d0.42596749
X-RAY DIFFRACTIONf_chiral_restr0.0399725
X-RAY DIFFRACTIONf_plane_restr0.0036899
X-RAY DIFFRACTIONf_dihedral_angle_d8.188666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.45231380.38571375X-RAY DIFFRACTION92.65
2.65-2.720.41071440.33791453X-RAY DIFFRACTION99.07
2.72-2.80.33011370.32451470X-RAY DIFFRACTION99.08
2.8-2.890.34121430.29991476X-RAY DIFFRACTION99.45
2.89-30.35431420.3051472X-RAY DIFFRACTION99.26
3-3.120.35171390.29351469X-RAY DIFFRACTION99.38
3.12-3.260.36831420.28741483X-RAY DIFFRACTION99.33
3.26-3.430.28911370.25661476X-RAY DIFFRACTION99.26
3.43-3.650.27711470.23341491X-RAY DIFFRACTION99.76
3.65-3.930.29111500.23271504X-RAY DIFFRACTION99.64
3.93-4.320.2781420.20351503X-RAY DIFFRACTION99.58
4.32-4.950.20811420.19741521X-RAY DIFFRACTION99.94
4.95-6.230.24011460.21011540X-RAY DIFFRACTION100
6.23-43.180.20951560.17861612X-RAY DIFFRACTION99.44

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