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- PDB-8upq: Campylobacter jejuni ketol-acid reductoisomerase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8upq
TitleCampylobacter jejuni ketol-acid reductoisomerase in complex with 2,3-dihydroxy-3-isovalerate.
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsOXIDOREDUCTASE / Inhibitor / Biofuel / Enzyme
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 / Ketol-acid reductoisomerase, C-terminal 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
: / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
DepositionOct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Ketol-acid reductoisomerase (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))
C: Ketol-acid reductoisomerase (NADP(+))
F: Ketol-acid reductoisomerase (NADP(+))
E: Ketol-acid reductoisomerase (NADP(+))
D: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,87918
Polymers224,9296
Non-polymers95112
Water9,800544
1
A: Ketol-acid reductoisomerase (NADP(+))
B: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2936
Polymers74,9762
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-123 kcal/mol
Surface area24680 Å2
MethodPISA
2
C: Ketol-acid reductoisomerase (NADP(+))
D: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2936
Polymers74,9762
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-117 kcal/mol
Surface area24850 Å2
MethodPISA
3
F: Ketol-acid reductoisomerase (NADP(+))
hetero molecules

F: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2936
Polymers74,9762
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12260 Å2
ΔGint-124 kcal/mol
Surface area24260 Å2
MethodPISA
4
E: Ketol-acid reductoisomerase (NADP(+))
hetero molecules

E: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2936
Polymers74,9762
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12010 Å2
ΔGint-118 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.822, 134.127, 126.862
Angle α, β, γ (deg.)90.000, 134.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11F-538-

HOH

21E-536-

HOH

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Components

#1: Protein
Ketol-acid reductoisomerase (NADP(+))


Mass: 37488.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ilvC / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5T0UG45
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-XAI / (2R)-2,3-dihydroxy-3-methylbutanoic acid


Mass: 134.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% v/v 2-propanol 0.1 M sodium citrate pH 5.5 20 % w/v PEG 4000

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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: 2.45→46.21 Å / Num. obs: 76291 / % possible obs: 97.1 % / Redundancy: 7.8 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 2.45→2.51 Å / Num. unique obs: 4942 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→42.19 Å / SU ML: 0.2875 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 2015 2.64 %
Rwork0.193 74256 -
obs0.1943 76271 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.12 Å2
Refinement stepCycle: LAST / Resolution: 2.45→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15368 0 60 544 15972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004515676
X-RAY DIFFRACTIONf_angle_d0.61521158
X-RAY DIFFRACTIONf_chiral_restr0.25382398
X-RAY DIFFRACTIONf_plane_restr0.00342754
X-RAY DIFFRACTIONf_dihedral_angle_d13.83085708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.29791220.22564942X-RAY DIFFRACTION91.34
2.51-2.580.26611760.2245310X-RAY DIFFRACTION97.65
2.58-2.650.27371300.21795364X-RAY DIFFRACTION97.85
2.65-2.740.30251490.22415314X-RAY DIFFRACTION97.87
2.74-2.840.28481440.21325321X-RAY DIFFRACTION98.01
2.84-2.950.27681470.22315353X-RAY DIFFRACTION97.97
2.95-3.080.27451450.22695301X-RAY DIFFRACTION97.97
3.08-3.250.29241360.21815333X-RAY DIFFRACTION97.7
3.25-3.450.25151320.20945283X-RAY DIFFRACTION96.85
3.45-3.720.25331390.18995228X-RAY DIFFRACTION95.43
3.72-4.090.21131340.16985422X-RAY DIFFRACTION98.67
4.09-4.680.1871550.15615381X-RAY DIFFRACTION98.59
4.68-5.890.21341510.17475371X-RAY DIFFRACTION97.75
5.9-42.190.20661550.17445333X-RAY DIFFRACTION96.25

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