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- PDB-7pct: BurG E232Q mutant (holo) in complex with enol-oxalacetate (15): B... -

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Basic information

Entry
Database: PDB / ID: 7pct
TitleBurG E232Q mutant (holo) in complex with enol-oxalacetate (15): Biosynthesis of cyclopropanol rings in bacterial toxins
ComponentsKetol-acid reductoisomerase
KeywordsLYASE / Pathogens / Natural Products / Toxins / Biosynthesis / Catalysis / Mutagenesis
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
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. / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (~{Z})-2-oxidanylbut-2-enedioic acid / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTrottmann, F. / Ishida, K. / Ishida, M. / Kries, H. / Groll, M. / Hertweck, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: Nat.Chem. / Year: 2022
Title: Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Authors: Trottmann, F. / Ishida, K. / Ishida-Ito, M. / Kries, H. / Groll, M. / Hertweck, C.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase
B: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,30412
Polymers77,4312
Non-polymers1,87210
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16780 Å2
ΔGint-158 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.290, 76.030, 78.230
Angle α, β, γ (deg.)90.000, 106.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ketol-acid reductoisomerase


Mass: 38715.715 Da / Num. of mol.: 2 / Mutation: E232Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: ilvC-2, BTH_II2094 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2T3G7, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 5 types, 752 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-Y3P / (~{Z})-2-oxidanylbut-2-enedioic acid


Mass: 132.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris; o.2 M NaAc, 16% PEG 4K, 2 mM NAD+, 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 139870 / % possible obs: 97.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.1
Reflection shellResolution: 1.35→1.45 Å / Rmerge(I) obs: 0.536 / Num. unique obs: 26615

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PCC

7pcc


Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.169 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 6993 5 %RANDOM
Rwork0.1561 ---
obs0.1573 132865 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.53 Å2 / Biso mean: 13.772 Å2 / Biso min: 7.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å2-0.88 Å2
2---0.92 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 122 749 6080
Biso mean--14.12 25.66 -
Num. residues----681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135431
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175018
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6447379
X-RAY DIFFRACTIONr_angle_other_deg1.4771.57711512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02920.37324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25215818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.311560
X-RAY DIFFRACTIONr_chiral_restr0.0710.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021245
X-RAY DIFFRACTIONr_rigid_bond_restr0.996310449
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 488 -
Rwork0.291 9279 -
all-9767 -
obs--92.64 %

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