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- PDB-7v8s: Crystal structure of cyclohexanone monooxygenase from T. municipa... -

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Basic information

Entry
Database: PDB / ID: 7v8s
TitleCrystal structure of cyclohexanone monooxygenase from T. municipale mutant L437T complexed with NADP+ and FAD in space group of P1211
ComponentsCyclohexanone Monooxygenase from Thermocrispum municipale
KeywordsFLAVOPROTEIN / cyclohexanone monooxygenase / directed evolution / regioselectivity
Function / homology
Function and homology information


cyclohexanone monooxygenase / cyclohexanone monooxygenase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cyclohexanone Monooxygenase from Thermocrispum municipale
Similarity search - Component
Biological speciesThermocrispum municipale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsLi, T. / Li, G.Y. / Yin, H.
Funding support China, 3items
OrganizationGrant numberCountry
Dalian Science and Technology Innovation Fund2020JJ25CY017 China
National Natural Science Foundation of China (NSFC)21807111 China
Doctoral Scientific Research Foundation of Liaoning Province2020-BS-013 China
CitationJournal: Acs Catalysis / Year: 2022
Title: Biocatalytic Baeyer-Villiger Reactions: Uncovering the Source of Regioselectivity at Each Evolutionary Stage of a Mutant with Scrutiny of Fleeting Chiral Intermediates.
Authors: Dong, Y.J. / Li, T. / Zhang, S.Q. / Sanchis, J. / Yin, H. / Ren, J. / Sheng, X. / Li, G.Y. / Reetz, M.T.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclohexanone Monooxygenase from Thermocrispum municipale
B: Cyclohexanone Monooxygenase from Thermocrispum municipale
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,53911
Polymers120,3662
Non-polymers3,1739
Water9,602533
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)61.122, 164.034, 62.052
Angle α, β, γ (deg.)90.000, 115.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyclohexanone Monooxygenase from Thermocrispum municipale


Mass: 60183.121 Da / Num. of mol.: 2 / Mutation: L437T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum municipale (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1L1QK40, cyclohexanone monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.1 % / Mosaicity: 0.784 ° / Mosaicity esd: 0.012 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97925 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 64544 / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.068 / Rrim(I) all: 0.125 / Χ2: 0.703 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.20.35533000.8430.2330.4260.55899.8
2.14-2.183.20.33131850.8610.2170.3970.59499.7
2.18-2.223.20.32232350.8670.210.3860.58199.6
2.22-2.263.20.3332200.8520.2150.3950.7599.1
2.26-2.313.20.173321510.1310.2180.70598.9
2.31-2.373.10.24532080.9190.1630.2950.62399
2.37-2.422.90.21731300.9060.1510.2650.63497.3
2.42-2.493.10.20631920.930.1380.2490.62997.6
2.49-2.563.40.18632410.9540.1190.2210.62499.9
2.56-2.653.40.1732390.9590.1080.2020.63599.9
2.65-2.743.40.19132480.930.1210.2270.79499.8
2.74-2.853.40.1432410.9680.090.1670.65899.8
2.85-2.983.30.12332460.970.080.1470.799.7
2.98-3.143.30.10332230.9820.0670.1230.70999.7
3.14-3.333.20.08832110.9850.0580.1060.73599.4
3.33-3.592.90.07731730.9970.0530.0940.86597.1
3.59-3.953.40.07332540.9870.0470.0870.91599.8
3.95-4.523.40.05732680.9940.0360.0670.78499.9
4.52-5.73.30.05532660.9940.0350.0650.6999.8
5.7-503.20.05932490.9940.0380.070.86698.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.526
Highest resolutionLowest resolution
Rotation27.78 Å2.19 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREP11.7.03phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m10

5m10


Resolution: 2.08→27.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.952 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 3269 5.1 %RANDOM
Rwork0.172 ---
obs0.1744 61218 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.44 Å2 / Biso mean: 20.677 Å2 / Biso min: 2.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0.42 Å2
2---0.7 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 2.08→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8306 0 207 533 9046
Biso mean--20.72 21.23 -
Num. residues----1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177941
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.65411950
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5818250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23251068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40621.66494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.197151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7541571
X-RAY DIFFRACTIONr_chiral_restr0.0610.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022131
LS refinement shellResolution: 2.081→2.135 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 194 -
Rwork0.213 4014 -
all-4208 -
obs--86.5 %

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