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

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Basic information

Entry
Database: PDB / ID: 8ytt
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: 2.14 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)63,5533
Polymers62,0221
Non-polymers1,5312
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-9 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.720, 53.220, 101.610
Angle α, β, γ (deg.)90.000, 96.720, 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: 62022.102 Da / Num. of mol.: 1
Mutation: F246Y,K326C,N386S,I388K,M390I,L426F,F432L,T433A,L435S,S438I,E488K,S489C,W490R,F505L
Source method: isolated from a genetically manipulated source
Details: Expressing His tag on N-end / 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.: 350 / 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: 49.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris (base)-Bicine pH 8.5; 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: 2.14→34.38 Å / Num. obs: 30933 / % possible obs: 99.25 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06703 / Net I/σ(I): 15.5
Reflection shellResolution: 2.14→2.217 Å / Rmerge(I) obs: 1.035 / Num. unique obs: 3054 / CC1/2: 0.764 / CC star: 0.931

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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: 2.14→34.38 Å / SU ML: 0.3213 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.9856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1487 4.81 %RANDOM
Rwork0.2111 29441 --
obs0.214 30928 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.65 Å2
Refinement stepCycle: LAST / Resolution: 2.14→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 101 350 4575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254331
X-RAY DIFFRACTIONf_angle_d0.60015883
X-RAY DIFFRACTIONf_chiral_restr0.0457634
X-RAY DIFFRACTIONf_plane_restr0.0035747
X-RAY DIFFRACTIONf_dihedral_angle_d10.5815573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.210.33921460.2792648X-RAY DIFFRACTION99.15
2.21-2.290.34191380.27042631X-RAY DIFFRACTION99.07
2.29-2.380.32631270.26032651X-RAY DIFFRACTION99.04
2.38-2.490.3521190.24892665X-RAY DIFFRACTION99.22
2.49-2.620.3491240.2562679X-RAY DIFFRACTION99.36
2.62-2.780.30851420.24232669X-RAY DIFFRACTION99.22
2.78-30.31481290.23772670X-RAY DIFFRACTION99.43
3-3.30.33251120.23972712X-RAY DIFFRACTION99.4
3.3-3.780.26181570.20652678X-RAY DIFFRACTION99.61
3.78-4.760.22481530.17562680X-RAY DIFFRACTION99.58
4.76-34.380.22851400.18952758X-RAY DIFFRACTION99.04

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