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- PDB-7ypd: Discovery and characterization of a new carbonyl reductase from R... -

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Basic information

Entry
Database: PDB / ID: 7ypd
TitleDiscovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering
ComponentsCarbonyl reductase
KeywordsOXIDOREDUCTASE / Carbonyl reductase / dimer / short-chain-reductase / fluorinated ketone reductase
Function / homology: / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / metal ion binding / cytoplasm / RHTO0S28e01354g1_1
Function and homology information
Biological speciesRhodotorula toruloides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsWatanabe, Y. / Asano, Y. / Hibi, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other government Japan
CitationJournal: To Be Published
Title: Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering
Authors: Watanabe, Y. / Asano, Y. / Hibi, M.
History
DepositionAug 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Carbonyl reductase
A: Carbonyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5285
Polymers53,4552
Non-polymers733
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-43 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.362, 65.084, 79.769
Angle α, β, γ (deg.)90.000, 99.834, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Carbonyl reductase


Mass: 26727.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodotorula toruloides (fungus) / Gene: RHTO0S_28e01354g / Production host: Escherichia coli (E. coli) / References: UniProt: A0A061BJP9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-Hydroxychloride pH8.5, 30%(w/v)PEG4,000, Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.267→40.56 Å / Num. obs: 106918 / % possible obs: 92.29 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.85 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.5
Reflection shellResolution: 1.267→1.312 Å / Num. unique obs: 5789 / Rsym value: 0.923

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WXB

3wxb


Resolution: 1.27→40.56 Å / SU ML: 0.1603 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 5445 5.09 %
Rwork0.1745 101473 -
obs0.1759 106918 92.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.27→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 3 559 4116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613792
X-RAY DIFFRACTIONf_angle_d0.90615194
X-RAY DIFFRACTIONf_chiral_restr0.082615
X-RAY DIFFRACTIONf_plane_restr0.0076677
X-RAY DIFFRACTIONf_dihedral_angle_d5.2603542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.3577770.37371220X-RAY DIFFRACTION33.49
1.28-1.30.37641030.36171984X-RAY DIFFRACTION54.65
1.3-1.310.37441410.34582264X-RAY DIFFRACTION62.08
1.31-1.330.38171370.35292580X-RAY DIFFRACTION70.94
1.33-1.350.35131530.33232853X-RAY DIFFRACTION78.24
1.35-1.360.36771570.32523082X-RAY DIFFRACTION84.88
1.36-1.380.351790.30963332X-RAY DIFFRACTION90.96
1.38-1.410.28741930.29593468X-RAY DIFFRACTION95.29
1.41-1.430.29922100.28713621X-RAY DIFFRACTION99.12
1.43-1.450.30781960.26543701X-RAY DIFFRACTION99.97
1.45-1.480.25131800.24783641X-RAY DIFFRACTION99.95
1.48-1.50.28231820.24013651X-RAY DIFFRACTION99.97
1.5-1.530.25171920.22413649X-RAY DIFFRACTION99.95
1.53-1.560.22142100.21223652X-RAY DIFFRACTION99.97
1.56-1.60.25841830.20223660X-RAY DIFFRACTION99.87
1.6-1.630.20891830.19353653X-RAY DIFFRACTION99.95
1.63-1.670.22571750.19193689X-RAY DIFFRACTION100
1.67-1.720.21782010.1893652X-RAY DIFFRACTION99.95
1.72-1.770.18791820.18793669X-RAY DIFFRACTION100
1.77-1.830.19971790.17763662X-RAY DIFFRACTION99.92
1.83-1.890.21171960.18143665X-RAY DIFFRACTION99.97
1.89-1.970.19441880.16833693X-RAY DIFFRACTION99.92
1.97-2.060.18132090.163668X-RAY DIFFRACTION99.97
2.06-2.170.18191990.1613667X-RAY DIFFRACTION99.95
2.17-2.30.1741940.14773643X-RAY DIFFRACTION99.95
2.3-2.480.16712110.15233648X-RAY DIFFRACTION99.82
2.48-2.730.20051980.16133699X-RAY DIFFRACTION99.97
2.73-3.120.19492040.15823692X-RAY DIFFRACTION99.9
3.12-3.940.16982160.13893671X-RAY DIFFRACTION99.51
3.94-40.560.16452170.1423744X-RAY DIFFRACTION99.82

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