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- PDB-5m10: Crystal structure of cyclohexanone monooxygenase from Thermocrisp... -

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Basic information

Entry
Database: PDB / ID: 5m10
TitleCrystal structure of cyclohexanone monooxygenase from Thermocrispum municipale in the oxidised state with a bound nicotinamide.
ComponentsCyclohexanone Monooxygenase from Thermocrispum municipale
KeywordsOXIDOREDUCTASE / Cyclohexanone monooxygenase Baeyer-Villiger monooxygenases Flavoenzymes
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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NICOTINAMIDE / Cyclohexanone Monooxygenase from Thermocrispum municipale
Similarity search - Component
Biological speciesThermocrispum municipale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsGomez-Castellanos, J.R. / Mattevi, A.
Funding support1items
OrganizationGrant numberCountry
EU Horizon 2020 Programme Research and Innovation actions H2020-LEIT BIO-2014-1635734
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2016
Title: Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase.
Authors: Romero, E. / Castellanos, J.R. / Mattevi, A. / Fraaije, M.W.
History
DepositionOct 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,55111
Polymers60,1951
Non-polymers2,35610
Water10,142563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-3 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.840, 113.630, 155.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 60195.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum municipale (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): str. K-12 substr. DH10B
References: UniProt: A0A1L1QK40*PLUS, cyclohexanone monooxygenase

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Non-polymers , 6 types, 573 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-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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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: 51.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl, 30 % PEG 4000

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Data collection

DiffractionMean temperature: 273.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.22→38.93 Å / Num. obs: 168622 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 9.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 8.36
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.21 / CC1/2: 0.701 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREP11.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→38.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.804 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16504 5115 3 %RANDOM
Rwork0.13086 168273 --
obs0.1319 163445 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.472 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å20 Å2
2---0.14 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.22→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 156 563 4873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0194597
X-RAY DIFFRACTIONr_bond_other_d0.0030.024192
X-RAY DIFFRACTIONr_angle_refined_deg2.781.9826290
X-RAY DIFFRACTIONr_angle_other_deg1.29139658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47123.636220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7615716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0151538
X-RAY DIFFRACTIONr_chiral_restr0.2690.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0215299
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.791.2462209
X-RAY DIFFRACTIONr_mcbond_other1.7741.2422206
X-RAY DIFFRACTIONr_mcangle_it2.081.882787
X-RAY DIFFRACTIONr_mcangle_other2.0941.8812788
X-RAY DIFFRACTIONr_scbond_it4.3651.5742388
X-RAY DIFFRACTIONr_scbond_other4.3621.5742388
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9062.2483493
X-RAY DIFFRACTIONr_long_range_B_refined4.36316.3965536
X-RAY DIFFRACTIONr_long_range_B_other4.16215.765400
X-RAY DIFFRACTIONr_rigid_bond_restr6.88838788
X-RAY DIFFRACTIONr_sphericity_free26.2965338
X-RAY DIFFRACTIONr_sphericity_bonded12.53358888
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 298 -
Rwork0.282 15418 -
obs--86.26 %

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