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- PDB-8yu0: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 8yu0
TitleStructure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus
ComponentsPutative flavin-binding monooxygenase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsQiang, G. / Zheng, Y.C. / Feng, L. / Yu, H.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21922804 China
CitationJournal: To Be Published
Title: Loop Engineering Facilitates the Nicotinamide Cofactors Utilization of BVMOs
Authors: Qiang, G. / Zheng, Y.C. / Feng, L. / Yu, H.L.
History
DepositionMar 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative flavin-binding monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5373
Polymers62,0061
Non-polymers1,5312
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-7 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.950, 53.220, 101.600
Angle α, β, γ (deg.)90.000, 97.133, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Putative flavin-binding monooxygenase


Mass: 62006.062 Da / Num. of mol.: 1
Mutation: L143P,F246Y,K326C,N386S,I388K,M390I,L426F,F432L,T433A,L435S,S438I,E488K,S489C,W490R,F505L
Source method: isolated from a genetically manipulated source
Details: N-end fusion of HIS tags / Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: P23_1101 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8XFY0
#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
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris (base)-Bicine pH 8.5; 20% (v/v) PEG 500*MME; 10% (w/v) PEG 20000; 0.09 M Halogens (Sodium fluoride; Sodium bromide; Sodium iodide).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→34.31 Å / Num. obs: 51717 / % possible obs: 98.85 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06287 / Net I/σ(I): 17.17
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.8599 / Num. unique obs: 4979 / CC1/2: 0.675 / CC star: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A37

6a37


Resolution: 1.8→34.31 Å / SU ML: 0.2414 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 2617 5.06 %
Rwork0.1929 49096 -
obs0.1952 51713 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 101 642 4831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314290
X-RAY DIFFRACTIONf_angle_d0.62155826
X-RAY DIFFRACTIONf_chiral_restr0.0463627
X-RAY DIFFRACTIONf_plane_restr0.0037738
X-RAY DIFFRACTIONf_dihedral_angle_d10.7313565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.38541310.29982458X-RAY DIFFRACTION93.47
1.83-1.870.32241230.26992531X-RAY DIFFRACTION99.33
1.87-1.910.32791420.25492553X-RAY DIFFRACTION97.57
1.91-1.950.30241350.24132573X-RAY DIFFRACTION99.23
1.95-1.990.27161550.23462526X-RAY DIFFRACTION98.39
1.99-2.040.24071470.21692586X-RAY DIFFRACTION98.56
2.04-2.10.24951280.20932538X-RAY DIFFRACTION99.48
2.1-2.160.25491350.20082591X-RAY DIFFRACTION98.8
2.16-2.230.25611540.20992597X-RAY DIFFRACTION99.17
2.23-2.310.26761320.20152583X-RAY DIFFRACTION99.31
2.31-2.40.25261320.2032569X-RAY DIFFRACTION99.52
2.4-2.510.28121290.20882624X-RAY DIFFRACTION99.46
2.51-2.640.24451350.21492594X-RAY DIFFRACTION99.53
2.64-2.810.28331560.21282592X-RAY DIFFRACTION99.46
2.81-3.030.27191430.20042585X-RAY DIFFRACTION99.82
3.03-3.330.24591310.19232641X-RAY DIFFRACTION99.78
3.33-3.810.21051280.16972636X-RAY DIFFRACTION99.57
3.81-4.80.19021430.15012620X-RAY DIFFRACTION99.1
4.8-34.310.20931380.18622699X-RAY DIFFRACTION99.09

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