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- PDB-7pci: BurG (holo) in complex with hydroxypyruvate-enol (8): Biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 7pci
TitleBurG (holo) in complex with hydroxypyruvate-enol (8): 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 / 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
(Z)-2,3-bis(oxidanyl)prop-2-enoic acid / IMIDAZOLE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6026
Polymers38,7171
Non-polymers8855
Water1,15364
1
A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,20412
Polymers77,4332
Non-polymers1,77010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area16720 Å2
ΔGint-142 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.670, 84.470, 46.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ketol-acid reductoisomerase


Mass: 38716.699 Da / Num. of mol.: 1
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, 69 molecules

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


Mass: 663.425 Da / Num. of mol.: 1 / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-74I / (Z)-2,3-bis(oxidanyl)prop-2-enoic acid / 2,3-dihydroxyacrylic acid / 2,3-dihydroxyprop-2-enoic acid / 67573738


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Imidazole; 20% PEG 6K, 2 mM NAD+, 5 mM MgCl2, 2 mM (8)

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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 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 23699 / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3335

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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: 1.9→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 12 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1181 5 %RANDOM
Rwork0.1988 ---
obs0.2001 22473 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.89 Å2 / Biso mean: 28.13 Å2 / Biso min: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1--4.12 Å2-0 Å2-0 Å2
2---2.03 Å20 Å2
3---6.15 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 58 65 2756
Biso mean--30.04 35.33 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132743
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172535
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.6433729
X-RAY DIFFRACTIONr_angle_other_deg1.1461.5765814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56420.429163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00115410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9731530
X-RAY DIFFRACTIONr_chiral_restr0.0430.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
X-RAY DIFFRACTIONr_rigid_bond_restr0.75435277
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 86 -
Rwork0.368 1646 -
all-1732 -
obs--98.58 %
Refinement TLS params.Method: refined / Origin x: 3.052 Å / Origin y: -27.552 Å / Origin z: 13.059 Å
111213212223313233
T0.045 Å20.0011 Å2-0.0003 Å2-0.0455 Å2-0.0003 Å2--0.005 Å2
L0.0614 °20.0161 °2-0.0027 °2-0.0447 °20.0153 °2--0.0102 °2
S-0.0002 Å °0.0018 Å °0.0169 Å °0.0004 Å °0.0025 Å °0.0047 Å °0.0055 Å °0.0035 Å °-0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 347
2X-RAY DIFFRACTION1A801 - 804

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