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- PDB-9phg: Ketoreductase Engineering for a Chemoenzymatic Fluorination and D... -

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Basic information

Entry
Database: PDB / ID: 9phg
TitleKetoreductase Engineering for a Chemoenzymatic Fluorination and Dynamic Kinetic Reduction Cascade
Componentsketoreductase
KeywordsOXIDOREDUCTASE / Rossmann fold / ketoreductase
Function / homology: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesSporobolomyces salmonicolor (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.479 Å
AuthorsHruza, A. / Chun, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Ketoreductase Engineering for a Chemoenzymatic Fluorination and Dynamic Kinetic Reduction Cascade
Authors: Chun, S.W. / Kosjek, B. / Cahn, J.K.B. / Makarewicz, A.M. / Cheung-Lee, W.L. / Verma, D. / Jones, C.M. / Hruza, A. / Forstater, J.H. / Li, S. / Gallagher, Q. / Murphy, G.S. / Moore, J.C.
History
DepositionJul 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ketoreductase
B: ketoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1426
Polymers77,5772
Non-polymers1,5654
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-26 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.599, 52.463, 83.861
Angle α, β, γ (deg.)75.95, 84.06, 66.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ketoreductase


Mass: 38788.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporobolomyces salmonicolor (yeast) / Production host: Escherichia coli (E. coli) / References: alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM ammonium acetate, 100 mM Bis-Tris methane, pH 5.5, 17% PEG10000

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.479→81.352 Å / Num. obs: 70301 / % possible obs: 62.4 % / Observed criterion σ(I): 1.2 / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.015 / Rpim(I) all: 0.015 / Rrim(I) all: 0.022 / Net I/σ(I): 23.3
Reflection shellResolution: 1.48→1.61 Å / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3515 / CC1/2: 0.984 / Rpim(I) all: 0.085 / Rrim(I) all: 0.12 / % possible all: 17.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.479→14.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.096
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 3489 -RANDOM
Rwork0.1742 ---
obs0.1752 70201 62.4 %-
Displacement parametersBiso mean: 21.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.6127 Å2-0.0713 Å2-0.0632 Å2
2--0.8299 Å2-0.771 Å2
3----0.2172 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.479→14.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5232 0 98 378 5708
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0119597HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3153SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1670HARMONIC5
X-RAY DIFFRACTIONt_it5500HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion701SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9803SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion15.49
LS refinement shellResolution: 1.48→1.55 Å
RfactorNum. reflection% reflection
Rfree0.2549 71 -
Rwork0.1869 --
obs0.1898 1405 9.86 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67480.2056-0.03040.32230.04280.69760.0299-0.0062-0.0696-0.0062-0.0025-0.0026-0.0696-0.0026-0.0273-0.03720.0024-0.0041-0.0085-0.014-0.0107-9.1145-14.946317.9435
20.313-0.056-0.02250.4778-0.07141.21070.0232-0.0276-0.0611-0.02760.0428-0.0291-0.0611-0.0291-0.066-0.01830.01420.0044-0.0174-0.0039-0.02775.2174-27.667-19.13
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 342
2X-RAY DIFFRACTION1{ A|* }A401 - 501
3X-RAY DIFFRACTION2{ B|* }B4 - 342
4X-RAY DIFFRACTION2{ B|* }B401 - 501

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