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- PDB-8yu4: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 8yu4
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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)63,5463
Polymers62,0951
Non-polymers1,4512
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-10 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.920, 53.230, 101.490
Angle α, β, γ (deg.)90.000, 96.855, 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: 62095.094 Da / Num. of mol.: 1
Mutation: L143P,A145S,A146S,L149W,K151I,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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / 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.: 216 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
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; 0.09 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: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.02→44.46 Å / Num. obs: 36825 / % possible obs: 99.27 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.04 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1405 / Net I/σ(I): 12.03
Reflection shellResolution: 2.02→2.092 Å / Rmerge(I) obs: 1.392 / Num. unique obs: 3633 / CC1/2: 0.627 / CC star: 0.878

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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: 2.02→44.46 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2595 1754 4.76 %
Rwork0.218 35064 -
obs0.2199 36818 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.36 Å2
Refinement stepCycle: LAST / Resolution: 2.02→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 97 216 4456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194343
X-RAY DIFFRACTIONf_angle_d0.54165897
X-RAY DIFFRACTIONf_chiral_restr0.0421635
X-RAY DIFFRACTIONf_plane_restr0.0026745
X-RAY DIFFRACTIONf_dihedral_angle_d15.0985596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.33581110.31822678X-RAY DIFFRACTION98.52
2.07-2.140.29541410.28342644X-RAY DIFFRACTION98.62
2.14-2.20.33741250.28262725X-RAY DIFFRACTION99.23
2.2-2.280.34411580.27112618X-RAY DIFFRACTION99.28
2.28-2.370.31721380.26412664X-RAY DIFFRACTION99.19
2.37-2.480.29591610.25422651X-RAY DIFFRACTION99.19
2.48-2.610.28191220.24682700X-RAY DIFFRACTION99.54
2.61-2.780.27731600.24262703X-RAY DIFFRACTION99.58
2.78-2.990.25761320.23662686X-RAY DIFFRACTION99.4
2.99-3.290.30031340.23392722X-RAY DIFFRACTION99.79
3.29-3.770.27671320.20792719X-RAY DIFFRACTION99.69
3.77-4.750.178980.17632777X-RAY DIFFRACTION99.83
4.75-44.460.22051420.18342777X-RAY DIFFRACTION98.85

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