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- PDB-7pcl: BurG (holo) in complex with 2-hydroxy-2-(hydroxy(isopropyl)amino)... -

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Basic information

Entry
Database: PDB / ID: 7pcl
TitleBurG (holo) in complex with 2-hydroxy-2-(hydroxy(isopropyl)amino)acetate (11): Biosynthesis of cyclopropanolrings 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 / valine biosynthetic process / isoleucine biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytosol
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-76I / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)79,15610
Polymers77,4332
Non-polymers1,7228
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-155 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.710, 84.040, 101.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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+)
#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-76I / (2S)-2-oxidanyl-2-[oxidanyl(propan-2-yl)amino]ethanoic acid / 2-hydroxy-2-(hydroxy(isopropyl)amino)acetate / (2S)-2-Hydroxy-2-[hydroxy(propan-2-yl)amino]acetic acid / 87438397


Mass: 149.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris; 0.8 M LiCl, 8% PEG 4K, 2 mM NADH, 5 mM MgCl2, 2 mM 11
PH range: 8.5

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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 EIGER2 X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 40538 / % possible obs: 97.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.5
Reflection shellResolution: 2.05→2.15 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5331

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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: 2.05→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.474 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2026 5 %RANDOM
Rwork0.188 ---
obs0.1895 38498 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.3 Å2 / Biso mean: 23.579 Å2 / Biso min: 13.81 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å2-0 Å2-0 Å2
2---0.7 Å20 Å2
3---3.93 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 112 220 5541
Biso mean--22.29 30.14 -
Num. residues----681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135423
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175016
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6457374
X-RAY DIFFRACTIONr_angle_other_deg1.1511.58111505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1220.4325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52315816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0931560
X-RAY DIFFRACTIONr_chiral_restr0.0460.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021245
X-RAY DIFFRACTIONr_rigid_bond_restr0.367310439
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 148 -
Rwork0.254 2821 -
all-2969 -
obs--99.1 %
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)
10.0085-0.0006-0.00340.00940.00150.00480.00120.0057-0.00050.0008-0.00150.00070.00040.00040.00030.02810.00030.00020.02170.00020.000114.841-18.248-15.808
20.0013-0.0004-0.00120.0025-0.0020.0042-0.00050.0005-0.0018-0.001-0.00070.001-0.00150.00210.00130.02860.00060.00030.022-0.00120.002523.043-47.617-15.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 341
2X-RAY DIFFRACTION1A801 - 804
3X-RAY DIFFRACTION2B2 - 342
4X-RAY DIFFRACTION2A805
5X-RAY DIFFRACTION2B801 - 803

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