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- PDB-7v8o: Crystal structure of cyclohexanone monooxygenase from T. municipa... -

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Basic information

Entry
Database: PDB / ID: 7v8o
TitleCrystal structure of cyclohexanone monooxygenase from T. municipale mutant L437T complexed with NADP+ and FAD in space group of P21221
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 / DI(HYDROXYETHYL)ETHER / Cyclohexanone Monooxygenase from Thermocrispum municipale
Similarity search - Component
Biological speciesThermocrispum municipale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 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)123,6159
Polymers120,3662
Non-polymers3,2497
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.301, 112.522, 156.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 22 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.73 % / Mosaicity: 0.927 ° / Mosaicity esd: 0.007 °
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: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 32723 / % possible obs: 99.6 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.041 / Rrim(I) all: 0.149 / Χ2: 0.897 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.812.70.48615790.9750.1390.5060.52198.8
2.8-2.8512.50.43216200.9790.1230.4490.52199.1
2.85-2.912.60.39215990.980.1120.4080.5399.1
2.9-2.9612.50.34915920.9850.10.3640.54599.4
2.96-3.0312.60.3316040.990.0950.3440.56799.2
3.03-3.112.60.28816120.990.0830.30.58199.4
3.1-3.1712.50.24616220.9910.0710.2570.63799.7
3.17-3.2612.30.23116260.9920.0680.2410.70699.8
3.26-3.3611.90.20615980.9930.0610.2150.759100
3.36-3.4611.10.17616220.9920.0550.1850.86399.8
3.46-3.59110.16116100.9940.050.1690.9498.5
3.59-3.7313.30.15416180.9960.0440.161.04799.9
3.73-3.913.90.14416500.9970.040.151.147100
3.9-4.1113.80.13516380.9970.0380.141.217100
4.11-4.3613.70.11116430.9980.0310.1151.227100
4.36-4.713.70.11116470.9980.0310.1151.30999.9
4.7-5.1713.30.116700.9980.0280.1041.16399.8
5.17-5.9212.60.09516590.9980.0280.0991.03299.9
5.92-7.4611.20.08417090.9970.0260.0881.01999.9
7.46-50130.06918050.9980.020.0721.315100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.471
Highest resolutionLowest resolution
Rotation28.13 Å2.86 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: 2.72→28.15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.888 / SU B: 15.302 / SU ML: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 1654 5.1 %RANDOM
Rwork0.2198 ---
obs0.2228 30973 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.49 Å2 / Biso mean: 32.385 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0 Å20 Å2
2--3.26 Å2-0 Å2
3----1.72 Å2
Refinement stepCycle: final / Resolution: 2.72→28.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8306 0 198 15 8519
Biso mean--33.66 16.71 -
Num. residues----1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138780
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177957
X-RAY DIFFRACTIONr_angle_refined_deg1.311.65411977
X-RAY DIFFRACTIONr_angle_other_deg1.1171.5818294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40651072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25721.66494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.525151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.51571
X-RAY DIFFRACTIONr_chiral_restr0.0510.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022129
LS refinement shellResolution: 2.72→2.79 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.325 123 -
Rwork0.266 1879 -
obs--83.21 %

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