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- PDB-7kh7: Crystal structure of Staphylococcus aureus ketol-acid reductoisom... -

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Basic information

Entry
Database: PDB / ID: 7kh7
TitleCrystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg2+, NADPH, and NSC116565
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsISOMERASE/Inhibitor / REDUCTOISOMERASE / INHIBITOR / COMPLEX / METAL BINDING PROTEIN / ISOMERASE / ISOMERASE-Inhibitor complex
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / amino acid 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 / Acetohydroxy acid isomeroreductase, catalytic 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NDP / Chem-WBY / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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 20, 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
A: Ketol-acid reductoisomerase (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,78211
Polymers75,7732
Non-polymers2,0099
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-148 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.922, 92.085, 101.645
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

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Protein , 1 types, 2 molecules AB

#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+)

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Non-polymers , 5 types, 70 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.04 %
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 EIGER2 X 1M / Detector: PIXEL / Date: Nov 1, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.62→48.84 Å / Num. obs: 20203 / % possible obs: 99.6 % / Redundancy: 13.44 % / Biso Wilson estimate: 54.4 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 2.62→2.74 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2352 / Rpim(I) all: 0.511 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w3k

5w3k


Resolution: 2.63→48.84 Å / SU ML: 0.3715 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.5494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3034 1990 9.91 %
Rwork0.2463 18088 -
obs0.2522 20078 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.1 Å2
Refinement stepCycle: LAST / Resolution: 2.63→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 0 127 61 5118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275205
X-RAY DIFFRACTIONf_angle_d0.53777076
X-RAY DIFFRACTIONf_chiral_restr0.0415765
X-RAY DIFFRACTIONf_plane_restr0.0038933
X-RAY DIFFRACTIONf_dihedral_angle_d17.13121853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.690.37791350.32551228X-RAY DIFFRACTION94.85
2.69-2.760.43321380.31151240X-RAY DIFFRACTION99.57
2.76-2.840.37931380.3071276X-RAY DIFFRACTION99.65
2.85-2.940.37121400.29481285X-RAY DIFFRACTION99.44
2.94-3.040.34061410.28781278X-RAY DIFFRACTION99.65
3.04-3.160.34161420.27151286X-RAY DIFFRACTION99.65
3.16-3.310.3721390.26991269X-RAY DIFFRACTION99.51
3.31-3.480.30511400.24961276X-RAY DIFFRACTION99.3
3.48-3.70.33761430.24671301X-RAY DIFFRACTION100
3.7-3.990.28291440.23291302X-RAY DIFFRACTION100
3.99-4.390.27741440.21511306X-RAY DIFFRACTION99.86
4.39-5.020.27971440.21751315X-RAY DIFFRACTION100
5.02-6.320.25621470.24441322X-RAY DIFFRACTION99.66
6.32-48.840.27331550.23141404X-RAY DIFFRACTION99.49

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