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- PDB-7f3p: Crystal structure of a nadp-dependent alcohol dehydrogenase mutan... -

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Basic information

Entry
Database: PDB / ID: 7f3p
TitleCrystal structure of a nadp-dependent alcohol dehydrogenase mutant in apo form
ComponentsNADP-dependent isopropanol dehydrogenase
KeywordsOXIDOREDUCTASE / alpha/beta dehydrogenase
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHan, X. / Bi, Y. / Wei, H.L. / Gao, J. / Li, Q. / Qu, G. / Sun, Z.T. / Liu, W.D.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Unlocking the Stereoselectivity and Substrate Acceptance of Enzymes: Proline-Induced Loop Engineering Test.
Authors: Qu, G. / Bi, Y. / Liu, B. / Li, J. / Han, X. / Liu, W. / Jiang, Y. / Qin, Z. / Sun, Z.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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: NADP-dependent isopropanol dehydrogenase
B: NADP-dependent isopropanol dehydrogenase
C: NADP-dependent isopropanol dehydrogenase
D: NADP-dependent isopropanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,0609
Polymers154,0554
Non-polymers1,0055
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16470 Å2
ΔGint-238 kcal/mol
Surface area45800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.848, 132.713, 135.230
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
NADP-dependent isopropanol dehydrogenase


Mass: 38513.715 Da / Num. of mol.: 4 / Mutation: P84S, I86L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Gene: adh / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14941, isopropanol dehydrogenase (NADP+)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Mosaicity: 2.058 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, NH4, citrate

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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: Aug 20, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 46897 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.264 / Rpim(I) all: 0.093 / Rrim(I) all: 0.281 / Χ2: 0.849 / Net I/σ(I): 3.2 / Num. measured all: 423007
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.6-2.698.10.8446150.8730.310.8970.468
2.69-2.88.40.72646150.9220.2640.7740.478
2.8-2.938.80.72746240.9410.2580.7720.49
2.93-3.0890.61346550.9580.2130.650.527
3.08-3.278.70.49446480.9650.1760.5250.571
3.27-3.539.60.3746540.980.1260.3910.722
3.53-3.889.90.29146790.9860.0970.3070.847
3.88-4.449.50.20947020.9890.0710.2211.163
4.44-5.589.10.17247560.9870.060.1821.375
5.58-2590.14549490.9910.0530.1551.672

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YKF

1ykf


Resolution: 2.6→24.77 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 2247 5.01 %
Rwork0.1808 42570 -
obs0.1836 44817 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 332.33 Å2 / Biso mean: 43.3172 Å2 / Biso min: 16.74 Å2
Refinement stepCycle: final / Resolution: 2.6→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10638 0 52 228 10918
Biso mean--85.14 39.37 -
Num. residues----1415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.690.3012240.206941664390100
2.69-2.80.27782250.206242004425100
2.8-2.930.30962180.223342154433100
2.93-3.080.24962240.216242304454100
3.08-3.270.30572180.211642224440100
3.27-3.530.25912230.194642264449100
3.53-3.880.24062240.181542564480100
3.88-4.440.18562280.153342854513100
4.44-5.580.21372290.15543064535100
5.58-24.770.20452340.16684464469899

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