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- PDB-8swm: Crystal structure of Campylobacter jejuni ketol-acid reductoisome... -

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Basic information

Entry
Database: PDB / ID: 8swm
TitleCrystal structure of Campylobacter jejuni ketol-acid reductoisomerase in complex with 2-acetolactate
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsOXIDOREDUCTASE / Inhibitor / Biofuel / Enzyme
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding
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
(2S)-2-hydroxy-2-methyl-3-oxobutanoic acid / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 19, 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 (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1096
Polymers35,8681
Non-polymers2405
Water19811
1
A: Ketol-acid reductoisomerase (NADP(+))
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)433,30472
Polymers430,41912
Non-polymers2,88660
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area79960 Å2
ΔGint-963 kcal/mol
Surface area136600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.715, 130.715, 130.715
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-405-

CL

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Components

#1: Protein Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / ...KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / Ketol-acid reductoisomerase type 1 / Ketol-acid reductoisomerase type I


Mass: 35868.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Gene: ilvC, CJE0735 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HVD9, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-X2X / (2S)-2-hydroxy-2-methyl-3-oxobutanoic acid


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


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium acetate, 0.1 M BIS-TRIS pH=5.5 and 17 % w/v PEG10000
PH range: 5.5-7.9

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→46.21 Å / Num. obs: 7593 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 81.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.038 / Rrim(I) all: 0.078 / Net I/σ(I): 16.9
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3 / Num. unique obs: 3286 / CC1/2: 0.918 / Rpim(I) all: 0.263 / Rrim(I) all: 0.542 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.34 Å / SU ML: 0.4325 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.8657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 755 9.95 %
Rwork0.2253 6836 -
obs0.2277 7591 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.45 Å2
Refinement stepCycle: LAST / Resolution: 3→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 13 11 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782435
X-RAY DIFFRACTIONf_angle_d0.84863297
X-RAY DIFFRACTIONf_chiral_restr0.0487377
X-RAY DIFFRACTIONf_plane_restr0.0054435
X-RAY DIFFRACTIONf_dihedral_angle_d16.5329864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.38841480.32141346X-RAY DIFFRACTION98.87
3.23-3.550.30821530.27411342X-RAY DIFFRACTION100
3.56-4.070.28841500.23881359X-RAY DIFFRACTION100
4.07-5.130.21581530.20951374X-RAY DIFFRACTION100
5.13-41.340.20911510.19541415X-RAY DIFFRACTION99.94

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