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- PDB-8yu2: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 8yu2
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 / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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)63,4553
Polymers62,0061
Non-polymers1,4492
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-12 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.690, 53.410, 102.630
Angle α, β, γ (deg.)90.000, 96.716, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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-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
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.05
Details: 0.1 M Tris (base)-Bicine pH 8.05; 20% (v/v) PEG 500*MME; 10% (w/v) PEG 20000; 0.2 M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D- Glucosamine)

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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: 2.63→38.85 Å / Num. obs: 17061 / % possible obs: 99.62 % / Redundancy: 6.7 % / Biso Wilson estimate: 75.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1364 / Net I/σ(I): 10.91
Reflection shellResolution: 2.63→2.724 Å / Rmerge(I) obs: 2.409 / Num. unique obs: 1666 / CC1/2: 0.342 / CC star: 0.714

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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: 2.63→38.85 Å / SU ML: 0.4844 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.3
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 937 5.49 %
Rwork0.2258 16115 -
obs0.2286 17052 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.97 Å2
Refinement stepCycle: LAST / Resolution: 2.63→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4094 0 97 122 4313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244292
X-RAY DIFFRACTIONf_angle_d0.5985827
X-RAY DIFFRACTIONf_chiral_restr0.0429628
X-RAY DIFFRACTIONf_plane_restr0.0035737
X-RAY DIFFRACTIONf_dihedral_angle_d17.4416591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.770.44321160.36822303X-RAY DIFFRACTION99.59
2.77-2.940.36311110.32032294X-RAY DIFFRACTION99.71
2.94-3.170.39091130.2982286X-RAY DIFFRACTION99.79
3.17-3.490.32671150.24942328X-RAY DIFFRACTION99.71
3.49-3.990.30071490.22872278X-RAY DIFFRACTION99.92
3.99-5.030.22262040.18172245X-RAY DIFFRACTION99.55
5.03-38.850.26121290.20642381X-RAY DIFFRACTION99.41

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