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- PDB-8jqk: Crystal structure of a carbonyl reductase SSCR mutant from Sporob... -

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Basic information

Entry
Database: PDB / ID: 8jqk
TitleCrystal structure of a carbonyl reductase SSCR mutant from Sporobolomyces Salmonicolor
ComponentsAldehyde reductase 2
KeywordsOXIDOREDUCTASE / SSCR / reductase / carbonyl reductase
Function / homologyalcohol dehydrogenase (NADP+) / : / alcohol dehydrogenase (NADP+) activity / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / Aldehyde reductase 2
Function and homology information
Biological speciesSporobolomyces salmonicolor (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZhang, H.L. / Li, Q. / Liu, W.D. / Chen, X. / Wu, Q.Q. / Zhu, D.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: Engineering a Carbonyl Reductase to Simultaneously Increase Activity Toward Bulky Ketone and Isopropanol for Dynamic Kinetic Asymmetric Reduction via Enzymatic Hydrogen Transfer
Authors: Zhang, H. / Chen, X. / Lv, T. / Li, Q. / Liu, W. / Feng, J. / Liu, X. / Yao, P. / Wu, Q. / Zhu, D.
History
DepositionJun 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde reductase 2
B: Aldehyde reductase 2


Theoretical massNumber of molelcules
Total (without water)75,1732
Polymers75,1732
Non-polymers00
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.740, 144.600, 48.190
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldehyde reductase 2 / Aldehyde reductase II / ARII


Mass: 37586.629 Da / Num. of mol.: 2 / Mutation: M242F/Q245T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporobolomyces salmonicolor (yeast)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.63→40.1 Å / Num. obs: 76825 / % possible obs: 96.8 % / Redundancy: 7.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.064 / Rrim(I) all: 0.179 / Χ2: 1 / Net I/σ(I): 11.4 / Num. measured all: 585665
Reflection shellResolution: 1.63→1.67 Å / % possible obs: 95 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.122 / Num. measured all: 44294 / Num. unique obs: 5612 / CC1/2: 0.557 / Rpim(I) all: 0.422 / Rrim(I) all: 1.2 / Χ2: 0.84 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→39.25 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 3814 4.97 %
Rwork0.2314 --
obs0.2333 76774 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 0 535 5726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045343
X-RAY DIFFRACTIONf_angle_d0.8857276
X-RAY DIFFRACTIONf_dihedral_angle_d5.36723
X-RAY DIFFRACTIONf_chiral_restr0.048827
X-RAY DIFFRACTIONf_plane_restr0.011932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.690.35683700.31517181X-RAY DIFFRACTION95
1.69-1.760.3223580.27837196X-RAY DIFFRACTION95
1.76-1.840.29644040.26447184X-RAY DIFFRACTION96
1.84-1.930.29273830.26577220X-RAY DIFFRACTION96
1.93-2.050.29943800.257274X-RAY DIFFRACTION97
2.05-2.210.30063740.23857302X-RAY DIFFRACTION97
2.21-2.430.26113880.23047324X-RAY DIFFRACTION97
2.43-2.790.25723760.22737357X-RAY DIFFRACTION98
2.79-3.510.26683810.22497443X-RAY DIFFRACTION98
3.51-39.250.23044000.2017479X-RAY DIFFRACTION98

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