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- PDB-4rg3: Epsilon-caprolactone-bound crystal structure of cyclohexanone mon... -

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Basic information

Entry
Database: PDB / ID: 4rg3
TitleEpsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Tight conformation
ComponentsCyclohexanone monooxygenase
KeywordsOXIDOREDUCTASE / Baeyer-Villiger monooxygenase / Baeyer-Villiger oxidation / biocatalysis / flavoprotein / green chemistry / protein engineering / Rossmann fold / FAD / NADPH / cyclohexanone / oxygen / Cytosolic (bacterial)
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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Caprolactone / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cyclohexanone monooxygenase
Similarity search - Component
Biological speciesRhodococcus sp. HI-31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsYachnin, B.J. / Berghuis, A.M.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Lactone-bound structures of cyclohexanone monooxygenase provide insight into the stereochemistry of catalysis.
Authors: Yachnin, B.J. / McEvoy, M.B. / MacCuish, R.J. / Morley, K.L. / Lau, P.C. / Berghuis, A.M.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6155
Polymers60,8091
Non-polymers1,8064
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.698, 67.060, 131.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cyclohexanone monooxygenase


Mass: 60808.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. HI-31 (bacteria) / Gene: chnB, chnB1 / Plasmid: pJW234 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: C0STX7, cyclohexanone monooxygenase

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Non-polymers , 5 types, 142 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-ECE / Caprolactone / Oxepan-2-one / Epsilon-Caprolactone


Mass: 114.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O2
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.02 Å3/Da / Density % sol: 39.15 % / Mosaicity: 0.802 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 60% PEG 3350, 0.1 M bicine, 0.1 M epsilon-caprolactone, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949216062007 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 23, 2011
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949216062007 Å / Relative weight: 1
ReflectionResolution: 1.94→25 Å / Num. all: 36410 / Num. obs: 36410 / % possible obs: 98.3 % / Redundancy: 13.4 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Χ2: 1.15 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obsRsym value
1.95-1.9812.716870.60591.4
1.98-2.0212.617130.6296.2
2.02-2.0612.617570.64395.3
2.06-2.112.517530.81596.30.8060.806
2.1-2.1512.517960.68698.10.6820.682
2.15-2.212.717710.689980.5980.598
2.2-2.2512.618100.93698.20.5240.524
2.25-2.3112.818210.98899.10.4580.458
2.31-2.3813.217880.76798.90.3390.339
2.38-2.4613.218110.827990.290.29
2.46-2.5413.318370.95299.10.2530.253
2.54-2.6513.718311.00499.30.2010.201
2.65-2.771418171.15199.40.1690.169
2.77-2.9114.318491.2299.50.1370.137
2.91-3.0914.618401.32699.30.1130.113
3.09-3.3314.518481.54599.80.1030.103
3.33-3.6714.518651.74399.70.090.09
3.67-4.214.318891.85799.80.0770.077
4.2-5.2814.119051.92999.80.0690.069
5.28-2513.220222.00199.80.0660.066

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UCL

3ucl


Resolution: 1.94→24.03 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.038 / SU ML: 0.114 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 3670 10.1 %RANDOM
Rwork0.1646 ---
all0.17 36235 --
obs0.17 36235 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.21 Å2 / Biso mean: 30.2361 Å2 / Biso min: 16.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.45 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.94→24.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 120 138 4318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194305
X-RAY DIFFRACTIONr_bond_other_d0.0010.023870
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9645895
X-RAY DIFFRACTIONr_angle_other_deg0.91138836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70723.211190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11215597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2541528
X-RAY DIFFRACTIONr_chiral_restr0.120.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
X-RAY DIFFRACTIONr_mcbond_it2.3262.8032117
X-RAY DIFFRACTIONr_mcbond_other2.3242.8022116
X-RAY DIFFRACTIONr_mcangle_it3.2014.1912645
LS refinement shellResolution: 1.944→1.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 286 -
Rwork0.215 2155 -
all-2441 -
obs-2441 90.64 %

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