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- PDB-7pcc: BurG in complex with Mg2+ and NAD+ (holo): Biosynthesis of cyclop... -

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Basic information

Entry
Database: PDB / ID: 7pcc
TitleBurG in complex with Mg2+ and NAD+ (holo): 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 / 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 ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,16110
Polymers76,5532
Non-polymers1,6088
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16540 Å2
ΔGint-155 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.490, 82.740, 100.870
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: 38276.270 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 (E. coli)
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine; 20% PEG 8K, 1 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: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 54278 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.8
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7832

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TSK

4tsk


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.035 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.717 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 2713 5 %RANDOM
Rwork0.1853 ---
obs0.1869 51548 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.04 Å2 / Biso mean: 22.772 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0 Å2
2---3.31 Å2-0 Å2
3---4.71 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5221 0 104 249 5574
Biso mean--25.14 28.92 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135428
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175024
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.6417379
X-RAY DIFFRACTIONr_angle_other_deg1.1981.57611526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.44220.4325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40815816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4141560
X-RAY DIFFRACTIONr_chiral_restr0.050.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021246
X-RAY DIFFRACTIONr_rigid_bond_restr0.622310452
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 197 -
Rwork0.283 3753 -
all-3950 -
obs--99.47 %
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)
10.03380.01240.00420.02990.0160.00950.00080.00030.00690.0002-0.0002-0.00040.0026-0.0008-0.00070.01020.0009-0.00010.0160.00030.001760.842364.956666.3335
20.03120.0138-0.00830.0376-0.0170.0093-0.00010.0026-0.00480.00080.0002-0.0005-0.0004-0.0009-0.00010.01070.0006-00.017-0.00030.001152.38135.802466.1081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 803
2X-RAY DIFFRACTION2B2 - 803

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