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- PDB-7v8r: Crystal structure of cyclohexanone monooxygenase from T. municipa... -

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Basic information

Entry
Database: PDB / ID: 7v8r
TitleCrystal structure of cyclohexanone monooxygenase from T. municipale mutant L437T complexed with NADP+ and FAD in space group of C2221
ComponentsCyclohexanone Monooxygenase from Thermocrispum municipale
KeywordsFLAVOPROTEIN / cyclohexanone monooxygenase / directed evolution / regioselectivity
Function / homologycyclohexanone monooxygenase / cyclohexanone monooxygenase activity / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / nucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cyclohexanone Monooxygenase from Thermocrispum municipale
Function and homology information
Biological speciesThermocrispum municipale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.764 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,33814
Polymers60,1831
Non-polymers2,15513
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.517, 113.787, 155.983
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cyclohexanone Monooxygenase from Thermocrispum municipale


Mass: 60183.121 Da / Num. of mol.: 1 / 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, 514 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.53 Å3/Da / Density % sol: 51.3 % / Mosaicity: 0.534 ° / Mosaicity esd: 0.004 °
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: 1.764→50 Å / Num. obs: 58633 / % possible obs: 97.4 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.036 / Rrim(I) all: 0.132 / Χ2: 0.741 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.811.80.49128860.9580.1470.5130.50996.9
1.8-1.8312.10.45828590.9610.1360.4780.52897.1
1.83-1.8712.20.42329160.970.1250.4410.54497.1
1.87-1.9112.40.4129100.970.1210.4280.55497.3
1.91-1.9512.20.35128630.9740.1040.3670.56797.4
1.95-1.9911.60.33429070.9690.1010.350.57697.3
1.99-2.0412.50.3227260.980.0930.3330.60691.8
2.04-2.1140.29729280.990.0820.3080.60697.8
2.1-2.1614.10.27329290.9920.0750.2830.63497.9
2.16-2.2314.10.25329320.9930.0690.2620.65398
2.23-2.31140.21929350.9950.060.2270.68598.1
2.31-2.413.90.19229310.9950.0530.1990.70298.3
2.4-2.5113.80.17129570.9950.0470.1780.73298.4
2.51-2.6413.50.14929690.9960.0420.1550.77798.6
2.64-2.8112.30.1329590.9930.0380.1360.84398.5
2.81-3.0313.10.11628740.9970.0330.1210.91394.6
3.03-3.3314.20.10229910.9980.0280.1061.02398.9
3.33-3.8113.90.08630130.9980.0240.0891.15399.2
3.81-4.813.20.0730570.9980.020.0731.06899.4
4.8-5013.10.0630910.9980.0170.0630.95896.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.425
Highest resolutionLowest resolution
Rotation28.45 Å1.9 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: 1.764→28.46 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.1024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2790 4.8 %RANDOM
Rwork0.1545 ---
obs0.156 55780 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.65 Å2 / Biso mean: 18.009 Å2 / Biso min: 9.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0 Å2-0 Å2
2--2.06 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.764→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 140 501 4794
Biso mean--25.79 25.15 -
Num. residues----529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134474
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174077
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6586100
X-RAY DIFFRACTIONr_angle_other_deg2.3441.589381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37421.587252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40115694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741537
X-RAY DIFFRACTIONr_chiral_restr0.0940.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025136
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021086
LS refinement shellResolution: 1.764→1.809 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 174 -
Rwork0.187 3934 -
all-4108 -
obs--92.67 %

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