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- PDB-8sxd: Campylobacter jejuni keto-acid reductoisomerase in complex with i... -

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Basic information

Entry
Database: PDB / ID: 8sxd
TitleCampylobacter jejuni keto-acid reductoisomerase in complex with intermediate and NADP+
ComponentsKetol-acid reductoisomerase
KeywordsOXIDOREDUCTASE / Ketol-acid reductoisomerase / enzyme / biofuel / drug target
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / 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. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE / Chem-NDP / : / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLin, X. / Lonhienne, T. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210101802 Australia
CitationJournal: Acs Catalysis / Year: 2024
Title: Mapping of the Reaction Trajectory catalyzed by Class I Ketol-Acid Reductoisomerase
Authors: Lin, X. / Lonhienne, T. / Lv, Y. / Kurz, J. / McGeary, R. / Schenk, G. / Guddat, L.W.
History
DepositionMay 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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)36,9527
Polymers35,8681
Non-polymers1,0846
Water64936
1
A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules

A: Ketol-acid reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,85621
Polymers107,6053
Non-polymers3,25118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area7790 Å2
ΔGint-76 kcal/mol
Surface area49380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.720, 130.720, 130.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-406-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ketol-acid reductoisomerase


Mass: 35868.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ilvC, CW563_00670 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5T0UG45, ketol-acid reductoisomerase (NADP+)

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Non-polymers , 6 types, 42 molecules

#2: Chemical ChemComp-WXU / 3-hydroxy-3-methyl-2-oxobutanoic acid


Mass: 132.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM 2-acetolactate, 10 mM NADP+, 0.1 M sodium HEPES pH=8.1, 20% w/v PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 29, 2022
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→46.22 Å / Num. obs: 11706 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 69.26 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.016 / Rrim(I) all: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 2.59→2.71 Å / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2 / Num. unique obs: 1407 / Rpim(I) all: 0.298 / Rrim(I) all: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LAT

7lat


Resolution: 2.59→37.74 Å / SU ML: 0.3668 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2448 1174 10.03 %
Rwork0.1911 10526 -
obs0.1966 11700 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.76 Å2
Refinement stepCycle: LAST / Resolution: 2.59→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 69 36 2545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01122561
X-RAY DIFFRACTIONf_angle_d1.21813474
X-RAY DIFFRACTIONf_chiral_restr0.054394
X-RAY DIFFRACTIONf_plane_restr0.0063450
X-RAY DIFFRACTIONf_dihedral_angle_d16.659911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.710.36761440.28671314X-RAY DIFFRACTION100
2.71-2.850.28921460.23371288X-RAY DIFFRACTION100
2.85-3.030.3211430.2561298X-RAY DIFFRACTION100
3.03-3.270.31861440.22871321X-RAY DIFFRACTION100
3.27-3.590.24951450.21731285X-RAY DIFFRACTION99.93
3.6-4.110.23511500.17851329X-RAY DIFFRACTION99.93
4.12-5.180.19461470.1711322X-RAY DIFFRACTION100
5.19-37.740.24031550.16741369X-RAY DIFFRACTION99.93

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