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

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Basic information

Entry
Database: PDB / ID: 8yrb
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 / Chem-NDP / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 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)63,5633
Polymers62,0321
Non-polymers1,5312
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.020, 53.220, 100.810
Angle α, β, γ (deg.)90.000, 96.485, 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: 62032.055 Da / Num. of mol.: 1
Mutation: L143P,A145S,A146S,N148H,K151V,F246Y,K326C,N386S,I388K,M390I,L426F,F432L,T433A,L435S,S438I,E488K,S489C,W490R,F505L
Source method: isolated from a genetically manipulated source
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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 0.1 M Tris (base)-Bicine pH 8.75; 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: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→34.18 Å / Num. obs: 53646 / % possible obs: 99.72 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08682 / Net I/σ(I): 13.8
Reflection shellResolution: 1.78→1.844 Å / Rmerge(I) obs: 1.359 / Num. unique obs: 5319 / CC1/2: 0.608

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Processing

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

Resolution: 1.78→34.18 Å / SU ML: 0.2533 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 2656 4.95 %
Rwork0.1866 50981 -
obs0.1886 53637 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.04 Å2
Refinement stepCycle: LAST / Resolution: 1.78→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 101 390 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994301
X-RAY DIFFRACTIONf_angle_d1.01575843
X-RAY DIFFRACTIONf_chiral_restr0.0632630
X-RAY DIFFRACTIONf_plane_restr0.0098740
X-RAY DIFFRACTIONf_dihedral_angle_d11.2762567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.33691580.29892638X-RAY DIFFRACTION100
1.81-1.850.32661550.28052611X-RAY DIFFRACTION100
1.85-1.880.34151320.27012728X-RAY DIFFRACTION99.97
1.88-1.930.36441150.28932659X-RAY DIFFRACTION99.32
1.93-1.970.33471480.24962708X-RAY DIFFRACTION99.72
1.97-2.020.25541310.22272628X-RAY DIFFRACTION100
2.02-2.070.26981220.23042693X-RAY DIFFRACTION99.68
2.07-2.140.25561190.22172698X-RAY DIFFRACTION99.89
2.14-2.20.23131660.19352676X-RAY DIFFRACTION100
2.2-2.280.24911290.21272648X-RAY DIFFRACTION99.28
2.28-2.370.2571290.19862688X-RAY DIFFRACTION99.96
2.37-2.480.25011280.18982698X-RAY DIFFRACTION100
2.48-2.610.23021540.19852654X-RAY DIFFRACTION100
2.61-2.780.25671630.19862692X-RAY DIFFRACTION99.93
2.78-2.990.24931520.18782684X-RAY DIFFRACTION100
2.99-3.290.24821180.19012722X-RAY DIFFRACTION99.89
3.29-3.770.2111380.16772694X-RAY DIFFRACTION99.4
3.77-4.750.19221550.14172703X-RAY DIFFRACTION99.51
4.75-34.180.15791440.16082759X-RAY DIFFRACTION98.84

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