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- PDB-8h61: Ketoreductase CpKR mutant - M2 -

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Basic information

Entry
Database: PDB / ID: 8h61
TitleKetoreductase CpKR mutant - M2
ComponentsMutant M2 of ketoreductase CpKR
KeywordsOXIDOREDUCTASE / Complex
Function / homology: / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / Chem-NDP / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, C. / Pan, J. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Research and Development Program of China2019YFA09005000 China
CitationJournal: To Be Published
Title: Computational redesign of a robust ketoreductase for asymmetric synthesis of enantiopure diltiazem precursor.
Authors: Chen, C. / Pan, J. / Xu, J.H.
History
DepositionOct 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mutant M2 of ketoreductase CpKR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2412
Polymers41,4951
Non-polymers7451
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-3 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.870, 77.960, 84.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mutant M2 of ketoreductase CpKR


Mass: 41495.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G8B6C8
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30 % (w/v) PEG3350 and 0.1 M Bis-Tris (pH 6.25)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→47.87 Å / Num. obs: 28234 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.042 / Rrim(I) all: 0.152 / Net I/σ(I): 15.9 / Num. measured all: 368922 / Scaling rejects: 870
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.8913.11.7532677520430.670.5021.8241.999.9
8.23-47.87110.03641623800.9990.0110.03849.499.4

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
PHENIX1.17_3644refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XWU

7xwu


Resolution: 1.9→41.67 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1241 4.84 %
Rwork0.1779 24392 -
obs0.1796 25633 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.68 Å2 / Biso mean: 30.5507 Å2 / Biso min: 13.05 Å2
Refinement stepCycle: final / Resolution: 1.9→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 48 227 2928
Biso mean--25.49 37.49 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.980.27771460.244426412787
1.98-2.070.27121400.200626612801
2.07-2.170.22811470.180726782825
2.18-2.310.23371430.190726502793
2.31-2.490.24011540.185926802834
2.49-2.740.20911310.187526852816
2.74-3.140.2141180.18127572875
3.14-3.950.20991130.165327672880
3.95-41.670.18981490.164328733022

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