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- PDB-7pcn: BurG (holo) in complex with gonyenediol (14), trigonic acid (6) a... -

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Basic information

Entry
Database: PDB / ID: 7pcn
TitleBurG (holo) in complex with gonyenediol (14), trigonic acid (6) and DMS: Biosynthesis of cyclopropanol rings in bacterial toxins
ComponentsKetol-acid reductoisomerase
KeywordsLYASE / Pathogens / Natural Products / Toxins / Biosynthesis / Catalysis
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
Chem-78I / Chem-7BI / (METHYLSULFANYL)METHANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)79,63614
Polymers77,4332
Non-polymers2,20312
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-150 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.880, 76.130, 79.110
Angle α, β, γ (deg.)90.000, 105.140, 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: 38716.699 Da / Num. of mol.: 2
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, 485 molecules

#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MSM / (METHYLSULFANYL)METHANE


Mass: 62.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-7BI / dimethyl-[(Z)-3,4,5-tris(oxidanyl)-5-oxidanylidene-pent-3-enyl]sulfanium


Mass: 193.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-78I / (2R)-2-oxidanyl-2-(1-oxidanylcyclopropyl)ethanoic acid


Mass: 132.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Inidazole; 10% PEG 8K, 2 mM NAD+, 5 mM MgCl2, 2 mM gonydiol (5)

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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: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 82909 / % possible obs: 98.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.3
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 13837

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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: 1.6→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.526 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 4145 5 %RANDOM
Rwork0.1337 ---
obs0.135 78752 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.12 Å2 / Biso mean: 17.986 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å2-0.55 Å2
2---0.38 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 140 473 5838
Biso mean--15.43 28.75 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135457
X-RAY DIFFRACTIONr_bond_other_d0.0040.0175053
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.6457422
X-RAY DIFFRACTIONr_angle_other_deg1.4171.58311593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01120.4325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12815819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0171560
X-RAY DIFFRACTIONr_chiral_restr0.0750.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026319
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021247
X-RAY DIFFRACTIONr_rigid_bond_restr1.589310510
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 309 -
Rwork0.237 5870 -
all-6179 -
obs--99.63 %

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