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- PDB-6isv: Structure of acetophenone reductase from Geotrichum candidum NBRC... -

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Basic information

Entry
Database: PDB / ID: 6isv
TitleStructure of acetophenone reductase from Geotrichum candidum NBRC 4597 in complex with NAD
ComponentsAcetophenone reductase
KeywordsOXIDOREDUCTASE / NAD binding
Function / homology
Function and homology information


oxidoreductase activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Acetophenone reductase
Similarity search - Component
Biological speciesGeotrichum candidum (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKoesoema, A.A. / Sugiyama, Y. / Senda, M. / Senda, T. / Matsuda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP16K05864 Japan
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2019
Title: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.
Authors: Koesoema, A.A. / Sugiyama, Y. / Xu, Z. / Standley, D.M. / Senda, M. / Senda, T. / Matsuda, T.
History
DepositionNov 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetophenone reductase
B: Acetophenone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2688
Polymers80,6802
Non-polymers1,5886
Water86548
1
A: Acetophenone reductase
B: Acetophenone reductase
hetero molecules

A: Acetophenone reductase
B: Acetophenone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,53616
Polymers161,3594
Non-polymers3,17712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area15580 Å2
ΔGint-235 kcal/mol
Surface area46630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.751, 104.751, 273.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-516-

HOH

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Components

#1: Protein Acetophenone reductase


Mass: 40339.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geotrichum candidum (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: M5A8V4
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: 20% PEG3350 0.1 M Sodium Citrate dihydrate / Temp details: 95

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 24, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.901 Å / Num. obs: 31670 / % possible obs: 100 % / Redundancy: 39.3 % / Rpim(I) all: 0.029 / Net I/σ(I): 23.9
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3471 / Rpim(I) all: 0.562

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.901 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.2718 1651 5.23 %
Rwork0.2181 --
obs0.221 31541 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 92 49 5028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075080
X-RAY DIFFRACTIONf_angle_d1.0276950
X-RAY DIFFRACTIONf_dihedral_angle_d8.6033050
X-RAY DIFFRACTIONf_chiral_restr0.056817
X-RAY DIFFRACTIONf_plane_restr0.006905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.57380.34171420.30042405X-RAY DIFFRACTION100
2.5738-2.65690.40181480.31432400X-RAY DIFFRACTION100
2.6569-2.75180.41421120.31692486X-RAY DIFFRACTION100
2.7518-2.8620.42421370.29832416X-RAY DIFFRACTION100
2.862-2.99220.33171190.27542466X-RAY DIFFRACTION100
2.9922-3.14990.34171360.27312451X-RAY DIFFRACTION100
3.1499-3.34730.32291350.25972465X-RAY DIFFRACTION100
3.3473-3.60560.2691350.2322493X-RAY DIFFRACTION100
3.6056-3.96830.25981390.20662486X-RAY DIFFRACTION100
3.9683-4.54220.22111460.16912527X-RAY DIFFRACTION100
4.5422-5.72130.23081390.18492559X-RAY DIFFRACTION100
5.7213-48.91020.22791630.18612736X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.3608 Å / Origin y: 51.4163 Å / Origin z: 13.3126 Å
111213212223313233
T0.5475 Å2-0.0647 Å2-0.0188 Å2-0.5229 Å20.0198 Å2--0.3994 Å2
L1.2755 °20.7877 °21.1867 °2-1.0586 °21.0623 °2--2.0044 °2
S0.1185 Å °-0.289 Å °-0.1464 Å °-0.1681 Å °-0.2064 Å °0.0399 Å °-0.0861 Å °-0.7288 Å °0.085 Å °
Refinement TLS groupSelection details: all

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