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- PDB-7pco: BurG E232Q mutant (holo) in complex with 2R,3R-2,3-dihydroxy-6-me... -

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Basic information

Entry
Database: PDB / ID: 7pco
TitleBurG E232Q mutant (holo) in complex with 2R,3R-2,3-dihydroxy-6-methyl-heptanoate (12): 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 / Ketol-acid reductoisomerase, C-terminal 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
(2R,3R)-6-methyl-2,3-bis(oxidanyl)heptanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 3, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,32312
Polymers77,4312
Non-polymers1,89210
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16540 Å2
ΔGint-164 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.730, 83.400, 104.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 , 6 types, 433 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-7FI / (2R,3R)-6-methyl-2,3-bis(oxidanyl)heptanoic acid / 2R,3R-2,3-dihydroxy-6-methyl-heptanoate


Mass: 176.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaAc; 0.05 M M MgAc2, 10% PEG 8K, 2 mM NAD+, 5 mM MgCl2, 2 mM (12)

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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 EIGER2 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: 1.55→30 Å / Num. obs: 93303 / % possible obs: 96.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.1
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2 / Num. unique obs: 16041

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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: 1.55→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.292 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 4665 5 %RANDOM
Rwork0.1762 ---
obs0.1775 88624 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.93 Å2 / Biso mean: 17.668 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å2-0 Å2
2---0.63 Å20 Å2
3---1.22 Å2
Refinement stepCycle: final / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 123 423 5765
Biso mean--18.85 26.48 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135442
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175044
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.6457396
X-RAY DIFFRACTIONr_angle_other_deg1.4021.58511572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.67720.37324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68915818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1771560
X-RAY DIFFRACTIONr_chiral_restr0.0730.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021247
X-RAY DIFFRACTIONr_rigid_bond_restr1.027310486
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 351 -
Rwork0.309 6652 -
all-7003 -
obs--99.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0244-0.0005-0.00070.0214-0.00420.00130.0011-0.0007-0.0063-0.0015-0.00090.004-0.00050.0005-0.00020.0016-0.0005-0.00050.0002-0.00010.031714.74914.56816.825
20.0174-0.0008-0.00480.01180.00290.0031-0.00020.00150.0066-0.00020.00070.00180.00130.0003-0.00050.00150.0006-0.00080.00050.00010.031523.30243.84116.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 341
2X-RAY DIFFRACTION1A801 - 803
3X-RAY DIFFRACTION1B401
4X-RAY DIFFRACTION2B-1 - 341
5X-RAY DIFFRACTION2A804
6X-RAY DIFFRACTION2B402 - 404

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