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- PDB-7pce: BurG (apo): Biosynthesis of cyclopropanol rings in bacterial toxins -

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Basic information

Entry
Database: PDB / ID: 7pce
TitleBurG (apo): 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3344
Polymers38,7171
Non-polymers6173
Water00
1
A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6688
Polymers77,4332
Non-polymers1,2346
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area13780 Å2
ΔGint-121 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.340, 61.340, 190.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#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 (E. coli)
References: UniProt: Q2T3G7, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 M Na/K-phosphate; 0.2 M NaCl; 50% PEG 200

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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: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 9678 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.2
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2 / Num. unique obs: 884

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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: 2.9→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 35.875 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 483 5 %RANDOM
Rwork0.2188 ---
obs0.2202 9184 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 79.874 Å2 / Biso min: 69.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å2-0.95 Å2-0 Å2
2---1.91 Å20 Å2
3---6.18 Å2
Refinement stepCycle: final / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 37 0 2527
Biso mean--98.46 --
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132574
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172391
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.6373499
X-RAY DIFFRACTIONr_angle_other_deg1.0671.5765481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7795324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.420.323155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11215394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6761529
X-RAY DIFFRACTIONr_chiral_restr0.0340.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02590
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 34 -
Rwork0.35 646 -
all-680 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -6.8509 Å / Origin y: 17.3794 Å / Origin z: 16.5367 Å
111213212223313233
T0.1494 Å2-0.0605 Å20.0322 Å2-0.0884 Å2-0.0258 Å2--0.056 Å2
L0.4389 °2-0.0106 °20.1298 °2-0.4985 °2-0.5359 °2--1.2181 °2
S-0.1266 Å °-0.0652 Å °0.0404 Å °-0.1587 Å °0.0713 Å °-0.0097 Å °0.0337 Å °0.0848 Å °0.0553 Å °

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