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- PDB-8jqj: Crystal structure of carbonyl reductase SSCR mutant 1 from Sporob... -

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Basic information

Entry
Database: PDB / ID: 8jqj
TitleCrystal structure of carbonyl reductase SSCR mutant 1 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: 1.4 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


Theoretical massNumber of molelcules
Total (without water)37,3451
Polymers37,3451
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.329, 52.353, 117.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37345.344 Da / Num. of mol.: 1 / Mutation: M242F/Q245T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporobolomyces salmonicolor (yeast) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES pH 7.5, 25% MPD, 25% PEG 1000 ,25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 57468 / % possible obs: 93.4 % / Redundancy: 9.2 % / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 8875 / CC1/2: 0.757 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.26 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.87 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2845 4.96 %
Rwork0.189 --
obs0.1895 57387 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 0 260 2821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042622
X-RAY DIFFRACTIONf_angle_d0.8093569
X-RAY DIFFRACTIONf_dihedral_angle_d5.248354
X-RAY DIFFRACTIONf_chiral_restr0.071407
X-RAY DIFFRACTIONf_plane_restr0.007454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.3013090.26135768X-RAY DIFFRACTION100
1.45-1.510.26463040.23475756X-RAY DIFFRACTION100
1.51-1.580.22952990.20645815X-RAY DIFFRACTION100
1.58-1.660.212960.20235782X-RAY DIFFRACTION100
1.66-1.770.24322650.20485203X-RAY DIFFRACTION89
1.77-1.90.21852560.19624864X-RAY DIFFRACTION84
1.92-2.090.21432500.19244715X-RAY DIFFRACTION93
2.09-2.40.18872560.18344931X-RAY DIFFRACTION84
2.4-3.020.2053110.18765924X-RAY DIFFRACTION100
3.02-46.260.17382990.17715784X-RAY DIFFRACTION94

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