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- PDB-7c1e: Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (... -

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Basic information

Entry
Database: PDB / ID: 7c1e
TitleCrystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Y127W)
ComponentsEpimerase domain-containing protein
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase(KpADH-Y127W) / NADPH
Function / homologyoxidoreductase 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesVanderwaltozyma polyspora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWu, Y.F. / Zhou, J.Y. / Liu, Y.F. / Xu, G.C. / Ni, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21776112 China
National Key R&D Program of China2018YFA0901700 China
Natural Science Foundation of Jiangsu ProvinceBK20171135 China
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Engineering an Alcohol Dehydrogenase from Kluyveromyces polyspora for Efficient Synthesis of Ibrutinib Intermediate
Authors: Wu, Y.F. / Zhou, J.Y. / Ni, J. / Zhu, C. / Sun, Z. / Xu, G.C. / Ni, Y.
History
DepositionMay 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)79,4314
Polymers77,9442
Non-polymers1,4872
Water14,214789
1
A: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7162
Polymers38,9721
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-4 kcal/mol
Surface area14610 Å2
MethodPISA
2
B: Epimerase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7162
Polymers38,9721
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-4 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.686, 102.686, 134.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Epimerase domain-containing protein / Alcohol dehydrogenase


Mass: 38972.180 Da / Num. of mol.: 2 / Mutation: Y127W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294) (fungus)
Strain: ATCC 22028 / DSM 70294 / Gene: Kpol_529p27 / Production host: Escherichia coli (E. coli) / References: UniProt: A7TM80
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 31% PEG 3350, 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.0, 1 mM NADP+

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 75717 / % possible obs: 93.9 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.014 / Rrim(I) all: 0.063 / Χ2: 0.959 / Net I/σ(I): 11.6 / Num. measured all: 1396456
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.7810.20.69326040.920.220.7290.8864.5
1.78-1.81110.59228020.9290.1820.6220.89869.8
1.81-1.8512.10.46929970.9610.1380.490.89474.6
1.85-1.8912.80.36833010.9750.1050.3840.92682.3
1.89-1.9313.80.29235810.9840.0810.3040.95589.3
1.93-1.9715.20.22339710.9910.0590.2310.99798
1.97-2.02190.16839950.9970.0390.1731.01399.7
2.02-2.07210.14340040.9980.0310.1461.047100
2.07-2.14210.12340540.9980.0270.1261.061100
2.14-2.220.70.1139850.9980.0240.1131.041100
2.2-2.2819.90.09740730.9980.0220.11.042100
2.28-2.3819.90.0940040.9980.0210.0931.064100
2.38-2.4821.30.0840270.9990.0180.0821.055100
2.48-2.6120.90.07340330.9990.0160.0751.05100
2.61-2.7819.90.06740610.9990.0150.0691.012100
2.78-2.9920.30.0640130.9990.0140.0620.957100
2.99-3.2921.10.05540380.9990.0120.0570.914100
3.29-3.7719.80.0540450.9990.0120.0520.84199.9
3.77-4.75210.04840260.9990.0110.050.76199.5
4.75-5019.50.04741030.9990.0110.0480.63199.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z2X

5z2x


Resolution: 1.75→25.67 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.1828 3628 4.97 %
Rwork0.1528 --
obs0.1543 72994 90.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.66 Å2 / Biso mean: 22.5436 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: final / Resolution: 1.75→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 146 789 6429
Biso mean--14.43 30.76 -
Num. residues----684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.2663640.20951387145147
1.77-1.80.24361000.18871513161352
1.8-1.820.2531740.19161721179559
1.82-1.850.21211090.17951864197364
1.85-1.880.21931130.17952107222072
1.88-1.910.1746990.17972364246380
1.91-1.940.20921320.1772689282190
1.94-1.980.2241500.16682831298197
1.98-2.020.21161420.16252897303999
2.02-2.060.21751450.163229613106100
2.06-2.10.22051640.15529243088100
2.1-2.150.17111360.152829803116100
2.15-2.210.17421630.152428893052100
2.21-2.270.19251280.146629833111100
2.27-2.330.17791840.1429293113100
2.33-2.410.1891610.144629413102100
2.41-2.490.17731840.145528883072100
2.49-2.590.15381560.139929483104100
2.59-2.710.18131470.145829463093100
2.71-2.850.1961560.149629673123100
2.85-3.030.17671440.154229483092100
3.03-3.270.17981680.156329333101100
3.27-3.590.16051520.149529383090100
3.59-4.110.16771470.137529793126100
4.11-5.170.13521490.13182921307099
5.18-25.670.22121610.182918307998

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