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- PDB-7y0k: Crystal structure of CpKR in complex with NADPH complex from Cand... -

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Basic information

Entry
Database: PDB / ID: 7y0k
TitleCrystal structure of CpKR in complex with NADPH complex from Candida parapsilosis
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / Ketoreductase / 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: 3.03 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
DepositionJun 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2382
Polymers41,4921
Non-polymers7451
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-2 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.046, 45.454, 48.921
Angle α, β, γ (deg.)67.440, 84.880, 68.280
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Epimerase domain-containing protein


Mass: 41492.137 Da / Num. of mol.: 1
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 (E. coli) / 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
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: 2.03 Å3/Da / Density % sol: 39.35 %
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: BL17B1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 5310 / % possible obs: 94.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Χ2: 0.902 / Net I/σ(I): 5.5 / Num. measured all: 17423
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.052.90.1642290.9570.1030.1940.51586.4
3.05-3.113.10.182410.9560.1130.2130.47388
3.11-3.1730.1632740.9540.1080.1960.48594.2
3.17-3.233.10.1622710.9770.1020.1920.56493.8
3.23-3.33.20.1432560.970.0920.1710.61497
3.3-3.383.20.1882730.9530.1220.2250.89295.5
3.38-3.463.30.1652910.9430.1010.1940.94395.7
3.46-3.563.20.1462410.9460.0950.1750.75892.7
3.56-3.6630.1692650.9430.1140.2041.26591.1
3.66-3.783.40.1252760.9760.0790.1480.7696.5
3.78-3.913.50.1642650.8980.1010.1931.57195.7
3.91-4.073.50.1092740.9820.0680.1280.87495.8
4.07-4.263.50.1052700.9870.0660.1250.91797.1
4.26-4.483.40.1032780.9680.0660.1230.96495.5
4.48-4.763.50.0932760.9880.0580.111.09695.5
4.76-5.133.40.0862530.9860.0560.1030.86592.3
5.13-5.643.10.0832700.9750.0560.1010.70392.2
5.64-6.463.50.0892800.9770.0560.1060.76898.6
6.46-8.133.50.0832620.9610.0520.0980.62294.6
8.13-503.40.0962650.9660.0590.1132.03293.3

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XWU

7xwu


Resolution: 3.03→27.84 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2.08 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 223 4.61 %
Rwork0.2004 4617 -
obs0.2038 4840 85.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.1 Å2 / Biso mean: 53.4475 Å2 / Biso min: 11.86 Å2
Refinement stepCycle: final / Resolution: 3.03→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 48 0 2617
Biso mean--64.98 --
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.03-3.820.3388940.22942051214576
3.82-27.840.23461290.18752566269594

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