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- PDB-4rg4: Epsilon-caprolactone-bound crystal structure of cyclohexanone mon... -

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Basic information

Entry
Database: PDB / ID: 4rg4
TitleEpsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Loose conformation
ComponentsCyclohexanone monooxygenase
KeywordsOXIDOREDUCTASE / Baeyer-Villiger monooxygenase / Baeyer-Villiger oxidation / biocatalysis / flavoprotein / green chemistry / protein engineering / Rossmann fold / FAD / NADPH / cyclohexanone / oxygen / Glutaraldehyde crystal cross-linking / 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 / PENTANEDIAL / Cyclohexanone monooxygenase
Similarity search - Component
Biological speciesRhodococcus sp. HI-31 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: Cyclohexanone monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6526
Polymers60,8091
Non-polymers1,8435
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.145, 67.028, 133.576
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, 58 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-PTD / PENTANEDIAL


Mass: 100.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.03 Å3/Da / Density % sol: 39.4 % / Mosaicity: 1.095 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40% PEG 3350, 0.1 M imidazole, 0.2 M epsilon-caprolactone; crystals were transferred to a fresh drop and cross-linked with glutaraldehyde, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 8, 2012 / Details: VariMax HF
RadiationMonochromator: Rotating copper anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→66.79 Å / Num. all: 16633 / Num. obs: 16633 / % possible obs: 94.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.03 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 0.949 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueΧ2% possible all
2.5-2.541.70.56730.50.82777.5
2.54-2.591.80.4317060.4310.89982.5
2.59-2.641.90.3897640.3890.85189.3
2.64-2.691.90.398130.390.90893.1
2.69-2.7520.3328010.3320.78894.1
2.75-2.822.10.3128340.3120.8496.5
2.82-2.892.40.2888480.2880.85794.5
2.89-2.962.50.2628000.2620.8595.9
2.96-3.052.80.2238380.2230.87793.4
3.05-3.153.10.1888060.1880.91896.3
3.15-3.263.50.158220.150.96893
3.26-3.393.70.1188170.1180.95493.6
3.39-3.553.90.0928200.0920.96993.8
3.55-3.734.10.0758380.0750.95594.8
3.73-3.974.40.0648630.0640.95197.5
3.97-4.2750.058860.050.92899.6
4.27-4.76.20.0448820.0440.986100
4.7-5.386.50.0449120.0440.879100
5.38-6.786.50.0489250.0480.919100
6.78-506.10.0329850.0321.17199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RG3

4rg3


Resolution: 2.51→66.79 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.466 / SU ML: 0.284 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 1678 10.1 %RANDOM
Rwork0.1825 ---
all0.1908 16591 --
obs0.1908 16591 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.39 Å2 / Biso mean: 39.2568 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2---1.39 Å20 Å2
3---2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.51→66.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 119 53 4044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194107
X-RAY DIFFRACTIONr_bond_other_d0.0010.023646
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9695632
X-RAY DIFFRACTIONr_angle_other_deg0.90938322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15923.657175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45515545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7691520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214697
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02980
X-RAY DIFFRACTIONr_mcbond_it2.7523.8272042
X-RAY DIFFRACTIONr_mcbond_other2.753.8272041
X-RAY DIFFRACTIONr_mcangle_it4.2065.7352549
LS refinement shellResolution: 2.507→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 99 -
Rwork0.326 872 -
all-971 -
obs-971 75.98 %

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