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- PDB-8yq3: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 8yq3
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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 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)63,4833
Polymers62,0321
Non-polymers1,4512
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-12 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.184, 53.052, 101.643
Angle α, β, γ (deg.)90.000, 96.975, 90.000
Int Tables number4
Space group name H-MP1211

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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-Gold(DE3)pLysS AG' (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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 0.1 M Tris (base)-Bicine pH 8.25; 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: Nov 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→100.891 Å / Num. obs: 18944 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.968 / CC star: 0.992 / Rmerge(I) obs: 0.1771 / Net I/σ(I): 6.29
Reflection shellResolution: 2.52→2.61 Å / Rmerge(I) obs: 1.202 / Num. unique obs: 1882 / CC1/2: 0.29 / CC star: 0.671 / % possible all: 99.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.52→100.891 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.864 / SU B: 19.209 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 3.096 / ESU R Free: 0.41
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3216 912 4.822 %RANDOM
Rwork0.2177 18001 --
all0.223 ---
obs-18913 99.889 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.958 Å2
Baniso -1Baniso -2Baniso -3
1-1.155 Å20 Å2-2.009 Å2
2---0.693 Å2-0 Å2
3---0.028 Å2
Refinement stepCycle: LAST / Resolution: 2.52→100.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 97 318 4464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124247
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163903
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.8445769
X-RAY DIFFRACTIONr_angle_other_deg0.5041.7899007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3895507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.576519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22910712
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.08310200
X-RAY DIFFRACTIONr_chiral_restr0.0650.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02984
X-RAY DIFFRACTIONr_nbd_refined0.2310.21180
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.24283
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22064
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.212
X-RAY DIFFRACTIONr_nbd_other0.1750.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.212
X-RAY DIFFRACTIONr_mcbond_it3.9525.1742034
X-RAY DIFFRACTIONr_mcbond_other3.9515.1742034
X-RAY DIFFRACTIONr_mcangle_it6.189.2852539
X-RAY DIFFRACTIONr_mcangle_other6.1799.2872540
X-RAY DIFFRACTIONr_scbond_it4.0595.6642213
X-RAY DIFFRACTIONr_scbond_other4.0585.6662214
X-RAY DIFFRACTIONr_scangle_it6.50710.2653230
X-RAY DIFFRACTIONr_scangle_other6.50610.2663231
X-RAY DIFFRACTIONr_lrange_it12.68852.4925332
X-RAY DIFFRACTIONr_lrange_other12.63252.6385271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.52-2.5850.452590.31513220.3213810.8870.9481000.315
2.585-2.6560.442610.37613090.3813710.7660.86599.92710.364
2.656-2.7330.433680.31712390.32313090.8780.90399.84720.301
2.733-2.8170.358660.27311880.27812550.9080.95199.92030.257
2.817-2.910.38590.24512100.25112710.8960.95699.84260.227
2.91-3.0120.323550.21111160.21611710.9270.9711000.196
3.012-3.1250.379540.2211230.22711770.90.9671000.204
3.125-3.2530.366490.19110610.19911120.9010.97599.82010.18
3.253-3.3970.25580.21710080.21910670.9530.96499.90630.209
3.397-3.5630.358570.2649720.2710320.8560.95499.70930.261
3.563-3.7550.391460.2469360.2529870.8910.95599.49340.241
3.755-3.9830.294370.2338750.2369130.9470.95999.89050.228
3.983-4.2570.303410.1838170.1888580.9360.9821000.192
4.257-4.5980.298400.1767800.1828220.9470.98199.75670.189
4.598-5.0350.246370.1377130.1427500.9680.9881000.151
5.035-5.6280.251450.1626360.1686810.9620.9861000.18
5.628-6.4950.405220.1975860.2046080.9270.9811000.213
6.495-7.9470.349210.1894960.1955170.950.9771000.211
7.947-11.2040.249240.1733840.1784080.9670.9791000.21
11.204-100.8910.248130.2962290.2922430.9760.94199.58850.43

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