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- PDB-7xwu: Ketoreductase CpKR mutant - M1 -

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Basic information

Entry
Database: PDB / ID: 7xwu
TitleKetoreductase CpKR mutant - M1
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / ketoreductase
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 / DI(HYDROXYETHYL)ETHER / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChen, C. / Zheng, Y.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. / Zheng, Y.C. / Pan, J. / Xu, J.H.
History
DepositionMay 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epimerase domain-containing protein
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6455
Polymers83,0482
Non-polymers1,5973
Water7,656425
1
A: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3763
Polymers41,5241
Non-polymers8522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-1 kcal/mol
Surface area14560 Å2
MethodPISA
2
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2702
Polymers41,5241
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.271, 53.562, 79.565
Angle α, β, γ (deg.)78.750, 81.650, 78.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Epimerase domain-containing protein


Mass: 41524.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Strain: CDC 317 / ATCC MYA-4646 / Gene: CPAR2_100480
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.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43031 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Χ2: 0.9 / Net I/σ(I): 11.1 / Num. measured all: 152835
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.70.27221120.9280.1640.3181.01796.8
2.03-2.073.70.26221710.870.1580.3071.08897.3
2.07-2.113.60.2121030.9450.1280.2461.03796.9
2.11-2.153.60.1821560.9630.110.2111.03297.5
2.15-2.23.60.14220910.9720.0870.1670.95197.4
2.2-2.253.50.13521480.970.0840.1591.10697.4
2.25-2.313.30.11921410.970.0760.1421.25696.9
2.31-2.373.60.1121230.9710.0670.1291.2797.9
2.37-2.443.70.0921790.9860.0540.1050.85297.9
2.44-2.523.60.07621300.990.0460.0890.84498
2.52-2.613.60.06821660.990.0420.080.74798.1
2.61-2.713.50.05821540.9920.0360.0690.73498.2
2.71-2.843.30.04921560.9930.0310.0580.65798
2.84-2.993.60.04721700.9930.0280.0550.60998.7
2.99-3.173.70.04221760.9940.0250.0490.63998.4
3.17-3.423.60.03821510.9930.0240.0450.60898.9
3.42-3.763.30.03421710.9940.0220.0410.59399
3.76-4.313.70.03521640.9950.0210.0410.59899.2
4.31-5.433.50.03321830.9920.020.0390.7399.4
5.43-503.60.03921860.9930.0230.0451.64799.3

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KWT

6kwt


Resolution: 2→46.84 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2189 5.09 %
Rwork0.2016 40820 -
obs0.2035 43009 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.15 Å2 / Biso mean: 32.8796 Å2 / Biso min: 4.46 Å2
Refinement stepCycle: final / Resolution: 2→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 103 425 5714
Biso mean--32.31 34.33 -
Num. residues----663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.040.30491280.2498242092
2.04-2.090.27891280.2409252497
2.09-2.140.32621280.2315257297
2.14-2.20.26791430.2279248997
2.2-2.260.24851190.2225258598
2.26-2.340.25431470.2299253897
2.34-2.420.27941390.2309257498
2.42-2.520.22891280.2238251298
2.52-2.630.28371440.2233257798
2.63-2.770.25771460.2153254498
2.77-2.950.25191300.207260198
2.95-3.170.25351530.2081257299
3.17-3.490.21171310.1974255099
3.49-40.20521450.1752259099
4-5.030.20191280.1694259599
5.04-46.840.21761520.1776257799

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